[med-svn] [python-mne] 90/376: DOC : adding first version of converted mne manual WIP
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:14 UTC 2015
This is an automated email from the git hooks/post-receive script.
yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit 5e744ee2cc38629f7708a35a27358eec2525c95d
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Sun Feb 20 16:26:52 2011 -0500
DOC : adding first version of converted mne manual WIP
---
doc/source/_static/navy.css | 4 +-
doc/source/contents.rst | 1 +
doc/source/index.rst | 4 +-
doc/source/manual/analyze.rst | 2730 ++++++++++++++++++++
doc/source/manual/browse.rst | 2605 +++++++++++++++++++
doc/source/manual/convert.rst | 2090 +++++++++++++++
doc/source/manual/cookbook.rst | 1058 ++++++++
doc/source/manual/forward.rst | 1202 +++++++++
doc/source/manual/index.rst | 23 +
doc/source/manual/intro.rst | 45 +
doc/source/manual/list.rst | 220 ++
doc/source/manual/matlab.rst | 714 +++++
doc/source/manual/mne.rst | 1323 ++++++++++
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doc/source/manual/morph.rst | 407 +++
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doc/source/manual/reading.rst | 145 ++
doc/source/manual/sampledata.rst | 769 ++++++
doc/source/manual/utilities.rst | 1362 ++++++++++
doc/source/tutorial.rst | 6 +-
99 files changed, 14701 insertions(+), 7 deletions(-)
diff --git a/doc/source/_static/navy.css b/doc/source/_static/navy.css
index f30a7fb..bb0c284 100644
--- a/doc/source/_static/navy.css
+++ b/doc/source/_static/navy.css
@@ -379,7 +379,7 @@ div.warning p.admonition-title {
color: white;
border-bottom: 1px solid #86989B;
font-weight: bold;
- background-color: #AFC1C4;
+ background-color: #05804A;
}
div.warning {
@@ -387,7 +387,7 @@ div.warning {
}
div.warning p.admonition-title {
- background-color: #000000;
+ background-color: #940000;
border-bottom-color: #940000;
}
diff --git a/doc/source/contents.rst b/doc/source/contents.rst
index 8ef1ff9..6eda6ce 100644
--- a/doc/source/contents.rst
+++ b/doc/source/contents.rst
@@ -8,6 +8,7 @@ Documentation Contents
:maxdepth: 2
getting_started.rst
+ manual/index
auto_examples/index.rst
tutorial.rst
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 5991ffc..8d0e8df 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -2,8 +2,8 @@
MNE Home
========
-MNE is a Python package for processing magnetoencephalography data
-(MEG) and electroencephalography (EEG) and. It includes python code
+MNE is a software package for processing magnetoencephalography data
+(MEG) and electroencephalography (EEG). It includes python code
for reading and writing FIF files produced by Neuromag MEG systems or
converted from other file formats.
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
new file mode 100644
index 0000000..a46fae4
--- /dev/null
+++ b/doc/source/manual/analyze.rst
@@ -0,0 +1,2730 @@
+
+
+.. _CACCICGI:
+
+====================
+Interactive analysis
+====================
+
+Overview
+########
+
+Interactive analysis of the MEG/EEG data and source estimates
+is facilitated by the mne_analyze tool.
+Its features include:
+
+- Viewing of evoked-response data or data
+ segments in a topographical layout.
+
+- Alignment of MEG and head coordinate frames.
+
+- Display of maps of the magnetic field and electric potentials.
+
+- Computation and display of cortically-constrained minimum-norm current
+ estimates and statistical maps derived from them. The solutions can
+ be displayed on folded and inflated cortical surfaces as well as
+ on curved and flattened surface patches.
+
+- Fitting of current dipoles to the data.
+
+- Connection to tkmedit (part
+ of FreeSurfer) to display data on MRI slices.
+
+- Production of QuickTime (TM) movies and graphics snapshots
+ in several image file formats.
+
+- Connection to cliplab (part of Elekta-Neuromag software) to
+ produce graphics reports, see :ref:`CACJEFAI`.
+
+- Inquiry and saving of source waveforms at selected surface
+ points or within ROIs defined by label files.
+
+- On-line morphing of the current distributions.
+
+- Output of snapshots in w file format.
+
+- Display of overlay data delivered in w and stc file formats.
+
+- Creation of ROI (label) files.
+
+- Viewing of continuous head-position data delivered by Elekta-Neuromag
+ software.
+
+.. _CHDJECCG:
+
+Command line options
+####################
+
+Since mne_analyze is
+primarily an interactive analysis tool, there are only a few command-line
+options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---cd <dir>**
+
+ Change to this directory before starting.
+
+**\---subject <name>**
+
+ Specify the default subject name for surface loading.
+
+**\---digtrig <name>**
+
+ Name of the digital trigger channel. The default value is 'STI
+ 014'. Underscores in the channel name will be replaced
+ by spaces.
+
+**\---digtrigmask <number>**
+
+ Mask to be applied to the raw data trigger channel values before considering
+ them. This option is useful if one wants to set some bits in a don't
+ care state. For example, some finger response pads keep the trigger
+ lines high if not in use, *i.e.*, a finger is
+ not in place. Yet, it is convenient to keep these devices permanently
+ connected to the acquisition system. The number can be given in
+ decimal or hexadecimal format (beginning with 0x or 0X). For example,
+ the value 255 (0xFF) means that only the lowest order byte (usually
+ trigger lines 1 - 8 or bits 0 - 7) will be considered.
+
+**\---visualizehpi**
+
+ Start mne_analyze in the restricted *head
+ position visualization* mode. For details, see :ref:`CHDEDFAE`.
+
+**\---dig <filename>**
+
+ Specify a file containing the head shape digitization data. This option
+ is only usable if the *head position visualization* position
+ visualization mode has been first invoked with the --visualizehpi
+ option.
+
+**\---hpi <filename>**
+
+ Specify a file containing the transformation between the MEG device
+ and head coordinate frames. This option is only usable if the *head
+ position visualization* position visualization mode has
+ been first invoked with the --visualizehpi option.
+
+**\---scalehead**
+
+ In *head position visualization* mode, scale
+ the average scalp surface according to the head surface digitization
+ data before aligning them to the scalp surface. This option is
+ recommended.
+
+**\---rthelmet**
+
+ Use the room-temperature helmet surface instead of the MEG sensor
+ surface when showing the relative position of the MEG sensors and
+ the head in the *head position visualization* mode.
+
+.. note:: Before starting mne_analyze the ``SUBJECTS_DIR`` environment variable has to be set.
+
+.. note:: Strictly speaking, trigger mask value zero would mean that all trigger inputs are ignored. However, for convenience, setting the mask to zero or not setting it at all has the same effect as 0xFFFFFFFF, *i.e.*, all bits set.
+
+.. note:: The digital trigger channel can also be set with the MNE_ENV_TRIGGER_CH environment variable. Underscores in the variable value will *not* be replaced with spaces by mne_analyze . Using the ``--digtrig`` option supersedes the MNE_ENV_TRIGGER_CH environment variable.
+
+.. note:: The digital trigger channel mask can also be set with the MNE_TRIGGER_CH_MASK environment variable. Using the ``--digtrigmask`` option supersedes the MNE_TRIGGER_CH_MASK environment variable.
+
+The main window
+###############
+
+.. _CACJABJI:
+
+.. figure:: picture.png
+ :alt: none
+
+ The main window of mne_analyze .
+
+The main window of mne_analyze shown
+in :ref:`CACJABJI` has the following components:
+
+- The menu bar;
+
+- Display area for a sample response;
+
+- Display of the estimated SNR, see :ref:`CACJFFEE`;
+
+- Display of a source waveform;
+
+- Message area, time-point selection text field, an ECD fit
+ button, a text field for selecting a vertex on the surface, and
+ a message text label;
+
+- Display area for the current estimates;
+
+- Controls for the current estimate display;
+
+- Topographical display of data.
+
+The menus
+#########
+
+The File menu
+=============
+
+The File shown in :ref:`CACJCBFI` contains the following items:
+
+.. _CACJCBFI:
+
+.. figure:: picture.png
+ :alt: none
+
+ The File menu.
+
+**Open...**
+
+ Load a new data set and an inverse operator. For details, see :ref:`CACBACHB`.
+
+**Open raw...**
+
+ Load epoch data from a raw data file. For details, see :ref:`CACDEDBI`.
+
+**Switch to data set...**
+
+ If multiple data sets or epochs from a raw data file are loaded,
+ this menu item brings up a list to switch between the data sets
+ or epochs.
+
+**Change working directory...**
+
+ Change the working directory of this program. This will usually
+ be the directory where your MEG/EEG data and inverse operator are located.
+
+**Load surface...**
+
+ Load surface reconstructions for the subject whose data you are analyzing,
+ see :ref:`CACFJICC`.
+
+**Load morphing surface...**
+
+ Load surface reconstructions of another subject for morphing, see :ref:`CACGBEIB`.
+
+**Load surface patch...**
+
+ Load a curved or flattened surface patch, see :ref:`CACFJICC`.
+
+**Load morphing surface patch...**
+
+ Load a curved or flattened surface patch for morphing, see :ref:`CACGBEIB`.
+
+**Load digitizer data...**
+
+ Load digitizer data for coordinate frame alignment, see :ref:`CACEHGCD`.
+
+**View continuous HPI data...**
+
+ Load a data file containing continuous head position information, see :ref:`CACIADAI`.
+
+**Manage overlays...**
+
+ Bring up the overlay manager to import data from stc and w files, see :ref:`CACFCHEC`.
+
+**Save bad channel selection**
+
+ Save the current bad channel selection created in the topographical data
+ display, see :ref:`CACEFBDE`.
+
+**Quit**
+
+ Quit the program.
+
+The Adjust menu
+===============
+
+The contents of the Adjust menu
+is shown in :ref:`CACFDIJJ`:
+
+.. _CACFDIJJ:
+
+.. figure:: picture.png
+ :alt: none
+
+ The Adjust menu.
+
+**Scales**
+
+ Adjust the scales of the data display.
+
+**Estimates...**
+
+ Adjust the properties of the displayed current estimates, see :ref:`CACBHDBF`.
+
+**Select trace layout...**
+
+ Select the layout for the topographical display, see :ref:`CACEFBDE`.
+
+**Lights...**
+
+ Adjust the lighting of the scenes in the main display and the viewer, see
+ Sections :ref:`CACBHDBF` and :ref:`CACEFFJF`.
+
+**Field mapping...**
+
+ Adjust the field mapping preferences, see :ref:`CACICDGA`.
+
+**Coordinate alignment...**
+
+ Establish a coordinate transformation between the MEG and MRI coordinate
+ frames, see :ref:`CACEHGCD`.
+
+The View menu
+=============
+
+The contents of the file menu is shown in :ref:`CACBFCGF`:
+
+.. _CACBFCGF:
+
+.. figure:: picture.png
+ :alt: none
+
+ The View menu.
+
+**Show viewer...**
+
+ Loads additional surfaces and pops up the viewer window. The functions
+ available in the viewer are discussed in :ref:`CACEFFJF`.
+
+**Show MRI viewer...**
+
+ Bring up the tkmedit program
+ to view MRI slices, see :ref:`CACCHCBF`.
+
+**Show coordinates...**
+
+ Show the coordinates of a vertex, see :ref:`CHDIEHDH`.
+
+**Show timecourse manager...**
+
+ Brings up the timecourse manager if some timecourses are available.
+ Timecourses are discussed in :ref:`CACCCFHH`.
+
+The Labels menu
+===============
+
+The contents of the Labels menu
+is shown in :ref:`CACHCDCF`. ROI analysis with help of labels
+is discussed in detail in :ref:`CACCCFHH`.
+
+.. _CACHCDCF:
+
+.. figure:: picture.png
+ :alt: none
+
+ The Labels menu.
+
+The label menu contains the following
+items:
+
+**Load label...**
+
+ Loads one label file for ROI analysis.
+
+**Load all labels...**
+
+ Loads all label files available in a directory for ROI analysis.
+
+**Load parcellation...**
+
+ Load cortical parcellation data produced by FreeSurfer from
+ directory $SUBJECTS_DIR/$SUBJECT/label and add the cortical regions
+ defined to the label list.
+
+**Show label list...**
+
+ Shows a list of all currently loaded labels for ROI analysis.
+
+**Discard all labels**
+
+ Discard all labels loaded so far. The label list window will be
+ hidden.
+
+**Clear marked vertices**
+
+ Clear the label outline or a label created interactively.
+
+The Dipoles menu
+================
+
+The contents of the dipoles menu is shown in :ref:`CACCJDAF`:
+
+.. _CACCJDAF:
+
+.. figure:: picture.png
+ :alt: none
+
+ The dipole fitting menu.
+
+**Setup fitting...**
+
+ Define the dipole fitting parameters, see :ref:`CACEDEGA`.
+
+**Show dipole list...**
+
+ Show the list of imported and fitted dipoles, see :ref:`CACGGAIA`.
+
+**Manage channel selections...**
+
+ Manage the selections of channels used in dipole fitting, see :ref:`CACIBHCI`.
+
+The Help menu
+=============
+
+The contents of the Help menu
+is shown in :ref:`CACGFEAF`:
+
+.. _CACGFEAF:
+
+.. figure:: picture.png
+ :alt: none
+
+ The Help menu.
+
+**On version...**
+
+ Displays the version and compilation date of the program.
+
+**On license...**
+
+ Displays the license information.
+
+**On GLX...**
+
+ Displays information about the OpenGL rendering context. If you experience
+ poor graphics performance, check that the window that pops up from
+ here says that you have a Direct rendering context .
+ If not, either your graphics card or driver software needs an update.
+
+**Why the beep?**
+
+ In some simple error situations, mne_analyze does
+ not popup an error dialog but refuses the action and rings the bell.
+ The reason for this can be displayed through this help menu item.
+
+.. _CACBACHB:
+
+Loading data
+############
+
+When you select Open... from
+the File menu the data loading
+dialog shown in :ref:`CACFHAIH` appears. It has four sections:
+
+- A standard file selection box.
+
+- List of available data sets. This part is automatically filled
+ in when a proper data file is selected from the file list. You can
+ select one or more data sets from this list. Multiple selection
+ works with help of the shift and control keys. If multiple data
+ sets are selected, the data set to be analyzed can be changed from
+ the data set list accessible through Switch to data set... in the File menu.
+
+- List of available inverse operator decompositions in the current
+ directory and its subdirectory called ``inv`` .
+
+- List of options:
+
+ - MRI/head transform source specifies a file to read the MRI/MEG coordinate
+ transformation information from. This is usually the inverse operator
+ file. However, you can also load data with inverse operator set
+ to <none> to view the data
+ as well as field and potential maps derived thereof. In this case
+ you need to specify the coordinate transformation file using the Select... button,
+ usually located in ``mri/T1-neuromag/sets`` under the subject's
+ FreeSurfer directory. The Default button
+ uses the default transformation file which must be called ``$SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-trans.fif`` .
+ This can be one of the MRI description files in ``mri/T1-neuromag/sets`` or
+ a transformation file stored from mne_analyze ,
+ see :ref:`CACEHGCD`.
+
+ - Use EEG average electrode ref. selects
+ whether the average electrode reference is applied to the data.
+ This is only available if the inverse operator is set to <none> .
+
+ - nave specifies the effective
+ number of averages to compute the SNR correctly. Usually your measurement
+ file contains this information.
+
+.. _CACFHAIH:
+
+.. figure:: picture.png
+ :alt: none
+
+ The open dialog.
+
+After the data set(s) has been selected, the following actions
+will take place:
+
+- The inverse operator will be loaded.
+
+- Baselines will be applied as specified in the scales dialog.
+
+- Projection will be applied to the data. If no inverse operator
+ is specified, the source for the projection data will be the data
+ file and the average EEG reference setting in the options. If an
+ inverse operator is included, the projection will be read from the
+ data file.
+
+- If an inverse operator is loaded, whitened data will be computed.
+
+- If an inverse operator is loaded, the SNR estimate as well
+ as the effective SNR will be computed from the whitened data and
+ displayed in the SNR window.
+
+- Waveforms will be shown in the topographical display as well
+ as in the sample channel display.
+
+If multiple data sets are loaded each data set has the following
+individual settings:
+
+- Amplitude and time scale settings,
+
+- Baseline,
+
+- Picked time point,
+
+- Sample channel to be displayed, and
+
+- MNE display preferences, see :ref:`CACHFFIJ`.
+
+If a data set has not been previously displayed, the currently
+active settings are copied to the data set.
+
+.. note:: If you double click on an inverse operator file name displayed in the Inverse operator list, the command used to produced this file will be displayed in a message dialog.
+
+.. _CACDEDBI:
+
+Loading epochs from a raw data file
+###################################
+
+Instead of an evoked-response data file it is possible to
+load epochs of data (single trials) from a raw data file. This option
+is invoked from File/Open raw... .
+The file selection box is identical to the one used for evoked responses
+(:ref:`CACFHAIH`) except that data set selector is replaced
+by the epoch selector show in :ref:`CACDCGIB`.
+
+.. _CACDCGIB:
+
+.. figure:: picture.png
+ :alt: none
+
+ The raw data epoch selector.
+
+The epoch selector contains the following controls:
+
+- The event specifier. Only events matching
+ this number are going to be considered.
+
+- The event source specifier. The event source can be either
+ the data file, *i.e.,* the digital trigger channel or
+ a event data file produced with mne_browse_raw or mne_process_raw ,
+ see Section 4.4.10. Using an event data file is useful
+ if, *e.g.*, the epochs to be processed epileptic spikes.
+
+- The time range specification. This determines the length of
+ the epoch with respect to the selected event.
+
+Once the settings have been accepted by clicking OK ,
+the first matching epoch will be displayed. You can switch between
+epochs using the data set list accessible through Switch to data set... in the File menu.
+
+.. _CACEFBDE:
+
+Data displays
+#############
+
+The MEG and EEG signals can be viewed in two ways:
+
+- A selection of MEG or EEG channel is
+ shown in a topographical layout.
+
+- One representative channel can be selected to the Sample channel display by clicking on a channel in the
+ topographical display.
+
+In both the sample channel display and the topographical
+display, current time point can be selected with a left mouse click.
+In addition, time point of interest can be entered numerically in
+the text box at the bottom left corner of the main display.
+
+.. _CACHBJAC:
+
+The topographical display
+=========================
+
+A selection of channels is always shown in the right most
+part of the main display. The topographical layout to use is selected
+from Adjust/Select trace layout... ,
+which brings up a window with a list of available layouts. The system-wide
+layouts reside in $MNE_ROOT/share/mne_analyze/lout. In addition
+any layout files residing in $HOME/.mne/lout are listed. The format
+of the layout files and selection of the default layout is discussed
+in Section 4.5.6.
+
+Several actions can be performed with the mouse in the topographical data
+display:
+
+**Left button click**
+
+ Selects a time point of interest.
+
+**Left button click with control key**
+
+ Selects a time point of interest and selects the channel under the pointer
+ to the sample channel display.
+
+**Left button drag with shift key**
+
+ Enlarges the view to contain only channels in the selected area.
+
+**Middle button click or drag**
+
+ Marks this channel as bad and clears all previously marked bad channel.
+ This action is only available if an inverse operator is *not* loaded.
+ An inverse operator dictates the selection of bad channels. The
+ current bad channel selection can be applied to the data from File/Save bad channel selection .
+
+**Middle button click or drag with control key**
+
+ Extends the bad channel selection without clearing the previously active
+ bad channels.
+
+**Right button**
+
+ Adjusts the channel selection used for dipole fitting in the same
+ way as the middle button selects bad channels. For more information
+ on channel selections, see :ref:`CACIBHCI`.
+
+.. _CACFGHBJ:
+
+The sample channel display
+==========================
+
+The sample channel display shows one of the measurement channels
+at the upper left corner of the mne_analyze user
+interface. A time point can be selected with a left mouse click.
+In addition, the following keyboard functions are associated with
+the sample channel display:
+
+**Down**
+
+ Change the sample channel to the next channel in the scanning order.
+
+**Up**
+
+ Change the sample channel to the previous channel in the scanning order.
+
+**Right**
+
+ Move forward in time by 1 ms.
+
+**Control Right**
+
+ Move forward in time by 5 ms.
+
+**Left**
+
+ Move backward in time by 1 ms.
+
+**Control Left**
+
+ Move backward in time by 5 ms.
+
+Scale settings
+==============
+
+The scales of the topographical and sample channel display
+can be adjusted from the Scales dialog
+which is invoked by selecting Adjust/Scales... from
+the menus. The Scales dialog
+shown in :ref:`CACJJCGD` has the following entries:
+
+**Analyze range min\s]**
+
+ Specifies the lower limit of the time range of data to be shown.
+
+**Analyze range max\s]**
+
+ Specifies the upper limit of the time range of data to be shown.
+
+**Use full time range**
+
+ If this box is checked, all data available in the data file will
+ be shown.
+
+**Baseline min\s]**
+
+ Specifies the lower time limit of the baseline.
+
+**Baseline max\s]**
+
+ Specifies the upper time limit of the baseline.
+
+**Baseline in use**
+
+ Baseline subtraction can be switched on and off from this button.
+
+**MEG amp min\T/cm]**
+
+ Lower limit of the vertical scale of planar gradiometer MEG channels.
+
+**MEG amp max\T/cm]**
+
+ Upper limit of the vertical scale of planar gradiometer MEG channels.
+
+**MEG axmult\m]**
+
+ The vertical scale of MEG magnetometers and axial gradiometers will
+ be obtained by multiplying the planar gradiometer vertical scale
+ limits by this value, given in centimeters.
+
+**EEG amp min [INLINE_EQUATIONV]**
+
+ Lower limit of the vertical scale of EEG channels.
+
+**EEG amp max [INLINE_EQUATIONV]**
+
+ Upper limit of the vertical scale of EEG channels.
+
+**Show stimulus channel**
+
+ Show the digital trigger channel data in the sample view together with
+ the sample channel.
+
+.. _CACJJCGD:
+
+.. figure:: picture.png
+ :alt: none
+
+ The Scales dialog.
+
+.. _CACFJICC:
+
+The surface display
+###################
+
+In mne_analyze , the current
+estimates are visualized on inflated or folded cortical surfaces.
+There are two visualization displays: the surface display, which
+is always visible, and the 3D viewer which is invoked from the Windows/Show viewer... menu selection, see :ref:`CACEFFJF`.
+
+A total of eight surfaces or patches can be assigned to the
+surface display:
+
+- The left and right hemisphere cortical
+ surfaces for the subject whose data you are analyzing. These surfaces
+ can be the inflated, white-matter, or pial surfaces. They are loaded
+ through the File/Load surface... menu
+ selection,
+
+- The left and right hemisphere cortical surfaces of another
+ subject or an alternative representation of the cortical surface
+ of the actual subject. For example, you can switch between the inflated
+ and folded (pial or white matter) cortical surfaces very easily.
+ These surfaces are loaded from the File/Load morphing surface... menu selection.
+
+- Left and right hemisphere curved or flat cortical patches
+ for the subject you are analyzing. This patch is loaded from the File/Load surface patch... menu selection. The full cortical
+ surfaces must be loaded first before loading the patches.
+
+- Patches for an another subject or another pair of patches
+ for the same subject through the File/Load morphing surface patch... menu selection. Again, the full
+ cortical surfaces must have been loaded first.
+
+.. _CHDIFFHJ:
+
+The surface selection dialog
+============================
+
+When File/Load surface... or File/Load morphing surface... is invoked, the surface selection dialog
+shown in :ref:`CACDGJDC` appears.
+
+.. _CACDGJDC:
+
+.. figure:: picture.png
+ :alt: none
+
+ The surface selection dialog.
+
+The dialog has the following components:
+
+**List of subjects**
+
+ This list contains the subjects available in the directory set with
+ the ``SUBJECTS_DIR`` environment variable.
+
+**List of available surfaces for the selected subject**
+
+ Lists the surfaces available for the current subject. When you click on
+ an item in this list, it appears in the Selected surface text field.
+
+**x-rotation (deg)**
+
+ Specifies the initial rotation of the surface around the *x* (left
+ to right) axis. Positive angle means a counterclockwise rotation
+ when the surface is looked at from the direction of the positive *x* axis.
+ Sometimes a more pleasing visualization is obtained when this rotations are
+ specified when the surface is loaded.
+
+**y-rotation (deg)**
+
+ Specifies the initial rotation of the surface around the *y* (back
+ to front) axis.
+
+**z-rotation (deg)**
+
+ Specifies the initial rotation of the surface around the *z* (bottom
+ to up) axis.
+
+The patch selection dialog
+==========================
+
+The surface patches are loaded with help of the patch selection
+dialog, which appears when File/Load surface patch... or File/Load morphing surface patch... is selected. This dialog,
+shown in :ref:`CACHEEJD`, contains a list of available patches
+and the possibility to rotate the a flat patch counterclockwise
+by the specified number of degrees from its original orientation.
+The patch is automatically associated with the correct hemisphere
+on the basis of the two first letters in the patch name (lh = left
+hemisphere, rh = right hemisphere).
+
+.. _CACHEEJD:
+
+.. figure:: picture.png
+ :alt: none
+
+ The patch selection dialog.
+
+.. _CACCABEA:
+
+Controlling the surface display
+===============================
+
+The main surface display has a section called Adjust view , which has the controls shown in :ref:`CACCFCGJ`:
+
+**L and R**
+
+ Select the left or right hemisphere surface loaded through File/Load surface... .
+
+**B**
+
+ Display the surfaces for both hemispheres.
+
+**M**
+
+ Display the surfaces loaded File/Load morphing surface... according to the L, R, and B hemisphere
+ selectors
+
+**P**
+
+ Select the patch associated with the currently selected surface. For this
+ to work, either L or R must be selected.
+
+**Option menu**
+
+ Select one of the predefined view orientations, see :ref:`CACCCGDB`, below.
+
+**Arrow buttons**
+
+ Rotate the surface by increments specified in degrees in the text
+ box next to the arrows.
+
+.. _CACCFCGJ:
+
+.. figure:: picture.png
+ :alt: none
+
+ Surface controls.
+
+The display can be also adjusted
+using keyboard shortcuts, which are available once you click in
+the main surface display with the left mouse button to make it active:
+
+**Arrow keys**
+
+ Rotate the surface by increments specified in degrees in the Adjust View section.
+
+**+**
+
+ Enlarge the image.
+
+**-**
+
+ Reduce the image.
+
+**=**
+
+ Return to the default size.
+
+**r**
+
+ Rotate the image one full revolution around z axis using the currently
+ specified rotation step. This is useful for producing a sequence
+ of images when automatic image saving is on, see :ref:`CACBEBGC`.
+
+**s**
+
+ Produces a raster image file which contains a snapshot of the currently
+ displayed image. For information on snapshot mode, see :ref:`CACBEBGC`.
+
+**.**
+
+ Stops the rotation invoked with the 'r' key, see
+ above.
+
+In addition, the mouse wheel or trackball can be used to
+rotate the image. If a trackball is available, *e.g.*,
+with the Apple MightyMouse, the image can be rotated up and down
+or left and right with the trackball. With a mouse wheel the image
+will rotated up and down when the wheel is rotated. Image rotation
+in the left-right direction is achieved by holding down the shift key
+when rotating the wheel. The shift key
+has the same effect on trackball operation.
+
+.. note:: The trackball and mouse wheel functionality is dependent on your X server settings. On Mac OSX these settings are normally correct by default but on a LINUX system some adjustments to the X server settings maybe necessary. Consult your system administrator or Google for details.
+
+.. _CHDIEHDH:
+
+Selecting vertices
+==================
+
+When you click on the surface with the left mouse button,
+the corresponding vertex number and the associated value will be
+displayed on the message line at the bottom of the display. In addition,
+the time course at this vertex will be shown, see :ref:`CHDGHDGE`.
+You can also select a vertex by entering the vertex number to the
+text field at the bottom of the display. If the MRI viewer is displayed and Track surface location in MRI is selected in the MRI viewer control dialog, the cursor in the MRI slices
+will also follow the vertex selection, see :ref:`CACCHCBF`.
+
+The View menu choice Show coordinates... brings up a window which shows
+the coordinates of the selected vertex on the *white matter* surface, *i.e.*,
+lh.white and rh.white FreeSurfer surfaces. If morphing surfaces
+have been loaded, the coordinates of both the subject being analyzed
+and those of the morphing subject will be shown. The Coordinates window
+includes the following lines:
+
+**MEG head**
+
+ Indicates the vertex location in the *MEG head* coordinates.
+ This entry will be present only if MEG/EEG data have been loaded.
+
+**Surface RAS (MRI)**
+
+ Indicates the vertex location in the *Surface RAS* coordinates.
+ This is the native coordinate system of the surfaces and this entry
+ will always be present.
+
+**MNI Talairach**
+
+ Shows the location in MNI Talairach coordinates. To be present,
+ the MRI data of the subject must be in the mgz format (usually true with
+ any recent FreeSurfer version) and the Talairach transformation
+ must be appropriately defined during the *FreeSurfer* reconstruction
+ workflow.
+
+**Talairach**
+
+ Shows the location in the *FreeSurfer* Talairach
+ coordinates which give a better match to the Talairach atlas.
+
+The above coordinate systems are discussed in detail in Section 5.2.
+
+.. note:: By default, the tksurfer program, part of the FreeSurfer package, shows the vertex locations on the *orig* rather than *white* surfaces. Therefore, the coordinates shown in mne_analyze and tksurfer are by default slightly different (usually by < 1 mm). To make the two programs consistent, you can start tksurfer with the ``-orig white`` option.
+
+.. _CACCCGDB:
+
+Defining viewing orientations
+=============================
+
+The list of viewing orientations available in the Adjust View section of the main surface display is controlled
+by a text file. The system-wide defaults reside in ``$MNE_ROOT/share/mne/mne_analyze/eyes`` .
+If the file ``$HOME/.mne/eyes`` exists, it is used instead.
+
+All lines in the eyes file starting with # are comments.
+The view orientation definition lines have the format:
+
+<name>:<Left>:<Right>:<Left up>:<Right up> ,
+
+where
+
+**<name>**
+
+ is the name of this viewing orientation,
+
+**<Left>**
+
+ specifies the coordinates of the viewing 'eye' location
+ for the left hemisphere, separated by spaces,
+
+**<Right>**
+
+ specifies the coordinates of the viewing location for the right
+ hemisphere,
+
+**<Left up>**
+
+ specifies the direction which is pointing up in the image for left hemisphere,
+ and
+
+**<Right up>**
+
+ is the corresponding up vector for the right hemisphere.
+
+All values are given in a coordinate system where positive *x* points
+to the right, positive *y* to the front, and
+positive *z* up. The lengths of the vectors specified
+for each of the four items do not matter, since parallel projection is
+used and the up vectors will be automatically normalized. The up
+vectors are usually 0 0 1, *i.e.*, pointing to
+the positive *z* direction unless the view is
+directly from above or below or if some special effect is desired.
+
+The names of viewing orientations should be less than 9 characters
+long. Otherwise, the middle pane of the main display will not be
+able to accommodate all the controls. The widths of the main window
+panes can be adjusted from the squares at the vertical sashes separating
+the panes.
+
+Adjusting lighting
+==================
+
+The scenes shown in the main surface display and the viewer,
+described in :ref:`CACEFFJF`, are lit by fixed diffuse ambient
+lighting and a maximum of eight light sources. The states, locations,
+and colors of these light sources can be adjusted from the lighting
+adjustment dialog shown in :ref:`CACDDHAI`, which can be
+accessed through the Adjust/Lights... menu
+choice. The colors of the lights can be adjusted numerically or
+using a color adjustment dialog accessible through the Color... buttons.
+
+.. _CACDDHAI:
+
+.. figure:: picture.png
+ :alt: none
+
+ The lighting adjustment dialog.
+
+.. _CACBEBGC:
+
+Producing output files
+======================
+
+.. _CACFBIHD:
+
+.. figure:: picture.png
+ :alt: none
+
+ Graphics output controls.
+
+Three types of output files can be produced from the main
+surface display using the graphics output buttons shown in :ref:`CACFBIHD`:
+
+**w files (w button)**
+
+ These files are simple binary files, which contain a list of vertex numbers
+ on the cortical surface and their current data values. The w files
+ will be automatically tagged with ``-lh.w`` and ``-rh.w`` .
+ They will only contain vertices which currently have a nonzero value.
+
+**Graphics snapshots (img button)**
+
+ These files will contain an exact copy of the image in tif or rgb
+ formats. The output format and the output mode is selected from
+ the image saving dialog shown in :ref:`CACCEFGI`. For more
+ details, see :ref:`CACIJFII`. If snapshot or automatic image
+ saving mode is in effect, thee img button
+ terminates this mode.
+
+**QuickTime (TM) movies (mov button)**
+
+ These files will contain a sequence of images as a QuickTime (TM) movie
+ file. The movie saving dialog shown in :ref:`CACFFBBD` specifies the
+ time range and the interval between the frames as well as the quality
+ of the movies, which is restricted to the range 25...100. The size
+ of the QuickTime file produced is approximately proportional to
+ the quality.
+
+.. _CACCEFGI:
+
+.. figure:: picture.png
+ :alt: none
+
+ File type selection in the image saving dialog.
+
+.. _CACFFBBD:
+
+.. figure:: picture.png
+ :alt: none
+
+ The controls in the movie saving dialog.
+
+.. _CACIJFII:
+
+Image output modes
+==================
+
+The image saving dialog shown in :ref:`CACCEFGI` selects
+the format of the image files produced and the image output mode.
+The buttons associated with different image format change the file
+name filter in the dialog to display files of desired type. However,
+the final output format is defined by the ending of the file name
+in the Selection text field as
+follows:
+
+**jpg**
+
+ JPEG (Joint Photographic Experts Group) format. Best quality jpeg is
+ always produced.
+
+**tif or tiff**
+
+ Uncompressed TIFF (Tagged Image File Format).
+
+**rgb**
+
+ RGB format.
+
+**pdf**
+
+ Portable Document File format.
+
+**png**
+
+ Portable Network Graphics format.
+
+.. note:: Only TIFF and RGB output routines are compiled into mne_analyze . For other output formats to work, the following programs must be present in your system: tifftopdf, tifftopnm, pnmtojpeg, and pnmtopng.
+
+There are three image saving modes which can be selected
+from the option menu labelled Output mode :
+
+**Single**
+
+ When OK is clicked one file containing
+ the present image is output.
+
+**Snapshot**
+
+ A new image file is produced every time ``s`` is pressed
+ in the image window, see Sections :ref:`CACCABEA` and :ref:`CACFDDCB`. The image file name is used as the stem of
+ the output files. For example, if the name is, ``sample.jpg`` ,
+ the output files will be ``sample_shot_001.jpg`` , ``sample_shot_002.jpg`` , *etc.*
+
+**Automatic**
+
+ A new image file is produced every time the image window changes.
+ The image file name is used as the stem of the output files. For
+ example, if the name is, ``sample.jpg`` , the output files
+ will be ``sample_001.jpg`` , ``sample_002.jpg`` , *etc.*
+
+.. _CACGBEIB:
+
+Morphing
+########
+
+The displayed surface distributions can be morphed to another
+subject's brain using the spherical morphing procedure,
+see Chapter 8. In addition to the morphing surfaces loaded
+through File/Load morphing surface... surface
+patches for the same subject can be loaded through File/Load morphing surface patch... . Switching between main and morphing
+surfaces is discussed in :ref:`CACCABEA`.
+
+Any labels displayed are visible on any of the surfaces displayed
+in the main surface display. Time points can be picked in any of
+the surfaces. As a result, the corresponding timecourses will be
+shown in the MNE amplitude window, see :ref:`CACCCFHH`.
+
+.. _CACEFFJF:
+
+The viewer
+##########
+
+.. _CACFDDCB:
+
+Overview
+========
+
+.. _CACJDFFH:
+
+.. figure:: picture.png
+ :alt: none
+
+ The viewer window with a visualization of MEG and EEG contour maps.
+
+When Windows/Show viewer... is
+selected, the following additional surfaces will be loaded:
+
+- The left and right hemisphere pial surfaces,
+
+- The surface representing the inner helmet shaped wall of the
+ dewar on which the MEG sensors are located,
+
+- The scalp surface, and
+
+- The BEM surfaces.
+
+The scalp surface is loaded from the file ``bem/`` <subject>``-head.fif`` under
+the subject's FreeSurfer directory. This surface is automatically
+prepared if you use the watershed algorithm as described in Section A.1.
+If you have another source for the head triangulation you can use
+the utility mne_surf2bem to create
+the fif format scalp surface file, see Section 5.6.
+
+If a file called ``bem/`` <subject>``-bem.fif`` under
+the subject's FreeSurfer directory is present, mne_analyze tries
+to load the BEM surface triangulations from there. This file can
+be a symbolic link to one of the ``-bem.files`` created
+by mne_prepare_bem_model , see Section 5.7.
+If the BEM file contains a head surface triangulation, it will be
+used instead of the one present in the ``bem/`` <subject>``-head.fif`` file.
+
+Once all required surfaces have been loaded, the viewer window
+shown in :ref:`CACJDFFH` pops up. In addition to the display
+canvas, the viewer has Adjust view controls
+similar to the main surface display and options for graphics output.
+The Adjust view controls do not
+have the option menu for standard viewpoints and has two additional
+buttons:
+
+The output options only include graphics output as snapshots
+(img ) or as movies (mov ).
+
+**Options...**
+
+ This button pops up the viewer options window which controls the appearance
+ of the viewer window.
+
+**Rescale**
+
+ This button adjusts the contour level spacing in the magnetic field and
+ electric potential contour maps so that the number of contour lines
+ is reasonable.
+
+**Reload**
+
+ Checks the modification dates of the surface files loaded to viewer and
+ reloads the data if the files have been changed. This is useful, *e.g.*,
+ for display of different BEM tessellations.
+
+The display can be also adjusted
+using keyboard shortcuts, which are available once you click in
+the viewer display with the left mouse button:
+
+**Arrow keys**
+
+ Rotate the surface by increments specified in degrees in the Adjust View section.
+
+**+**
+
+ Enlarge the image.
+
+**-**
+
+ Reduce the image.
+
+**=**
+
+ Return to the default size.
+
+**r**
+
+ Rotate the image one full revolution around z axis using the currently
+ specified rotation step. This is useful for producing a sequence
+ of images when automatic image saving is on, see :ref:`CACBEBGC`.
+
+**s**
+
+ Produces a image file which contains a snapshot of the currently displayed
+ image. For information on snapshot mode, see :ref:`CACBEBGC`.
+
+**.**
+
+ Stops the rotation invoked with the 'r' key, see
+ above.
+
+The left mouse button can be also used to inquire estimated
+magnetic field potential values on the helmet and head surfaces
+if the corresponding maps have been calculated and displayed.
+
+In addition, the mouse wheel or trackball can be used to
+rotate the image. If a trackball is available, *e.g.*,
+with the Apple MightyMouse, the image can be rotated up and down
+or left and right with the trackball. With a mouse wheel the image
+will rotated up and down when the wheel is rotated. Image rotation
+in the left-right direction is achieved by holding down the shift key
+when rotating the wheel. The shift key
+has the same effect on trackball operation.
+
+.. note:: The trackball and mouse wheel functionality is dependent on your X server settings. On Mac OSX these settings are normally correct by default but on a LINUX system some adjustments to the X server settings maybe necessary. Consult your system administrator or Google for details.
+
+.. _CACHGDEA:
+
+Viewer options
+==============
+
+.. figure:: picture.png
+ :alt: none
+
+ The viewer options window
+
+The viewer options window shown above contains three main
+sections to control the appearance of the viewer:
+
+- Selectors for various items to show,
+
+- Options for some of the items, and
+
+- Control of the color and transparency of the items, if applicable.
+ The color can be adjusted either by entering numeric values in the
+ range 0...1 or with help of a color editor which appears from the Color... button.
+ The transparency value has the same range as the other color components,
+ zero indicating a fully transparent (invisible) surface and one a
+ fully opaque one.
+
+The available items are:
+
+**Left hemi**
+
+ The pial surface of the left hemisphere. This surface can be made transparent.
+ Naturally, this surface will only be visible if the scalp is made
+ transparent.
+
+**Right hemi**
+
+ The pial surface of the right hemisphere.
+
+**Inner skull**
+
+ The inner skull surface. This surface can be made transparent. If parts
+ of the pial surface are outside of the inner skull surface, they will
+ be visible, indicating that the inner skull surface is obviously inside
+ the inner skull. Note that this criterion is more conservative than
+ the one imposed during the computation of the forward solution since
+ the source space points are located on the white matter surface
+ rather than on the pial surface. This surface can be displayed only
+ if the BEM file is present, see :ref:`CACFDDCB`.
+
+**Outer skull**
+
+ The outer skull surface. This surface can be made transparent. This surface can
+ be displayed only if the BEM file is present and contains the outer
+ skull surface, see :ref:`CACFDDCB`.
+
+**Scalp**
+
+ The scalp surface. This surface can be made transparent. The display
+ of this surface requires that the scalp triangulation file is present,
+ see :ref:`CACFDDCB`.
+
+**Digitizer data**
+
+ The 3D digitizer data collected before the MEG/EEG acquisition. These
+ data are loaded from File/Load digitizer data... .
+ The display can be restricted to HPI coil locations and cardinal
+ landmarks with the option. The digitizer points are shown as disks
+ whose radius is equal to the distance of the corresponding point
+ from the scalp surface. Points outside the scalp are shown in red
+ and those inside in blue. Distinct shades of cold and warm colors
+ are used for the fiducial landmarks. The HPI coils are shown in
+ green. Further information on these data and their use in coordinate
+ system alignment is given in :ref:`CACEHGCD`.
+
+**Helmet**
+
+ The MEG measurement surface, *i.e.*, inner surface
+ of the dewar.
+
+**EEG electrodes**
+
+ The EEG electrode locations. These will be only available if your data
+ set contains EEG channels.
+
+**MEG sensors**
+
+ Outlines of MEG sensors.
+
+**MEG field map**
+
+ Estimated contour map of the magnetic field component normal to the
+ helmet surface or normal to the scalp, see :ref:`CACICDGA`.
+
+**EEG potential map**
+
+ Interpolated EEG potential map on the scalp surface, see :ref:`CACICDGA`.
+
+**Activity estimates**
+
+ Current estimates on the pial surface.
+
+.. _CACICDGA:
+
+Magnetic field and electric potential maps
+##########################################
+
+Overview
+========
+
+In mne_analyze , the magnetic
+field and potential maps displayed in the viewer window are computed
+using an MNE-based interpolation technique. This approach involves
+the following steps:
+
+- Establish an inverse operator to compute
+ a minimum norm solution on a spherical surface using a spherically
+ symmetric forward model. Instead of assuming a discrete grid of
+ sources, a continuous distribution of tangential currents is employed.
+ In this case the lead field dot products can be computed in closed
+ form. Separate solutions are computed for MEG and EEG.
+
+- The normal component of the magnetic field or the electric
+ potential on the helmet or head surface is computed from the MEG-based
+ and EEG-based MNE. Since the MNE predicts the original measurements
+ accurately, it can also interpolate and extrapolate the data reliably.
+ The grid of interpolation or extrapolation points can be located
+ on the helmet or scalp surface for MEG and on the scalp surface
+ for EEG.
+
+The magnetic field and potential maps appear automatically
+whenever they are enabled from the viewer options, see :ref:`CACHGDEA`.
+
+.. _CACGFBCI:
+
+Technical description
+=====================
+
+Let INLINE_EQUATION be an MEG or an EEG
+signal at channel INLINE_EQUATION. This signal
+is related to the primary current distribution INLINE_EQUATIONthrough
+the lead field INLINE_EQUATION:
+
+.. math:: 1 + 1 = 2
+
+where the integration space INLINE_EQUATION in
+our case is a spherical surface. The oblique boldface characters
+denote three-component locations vectors and vector fields.
+
+The inner product of two leadfields is defined as:
+
+.. math:: 1 + 1 = 2
+
+These products constitute the Gram matrix INLINE_EQUATION.
+The minimum -norm estimate can be expressed as a weighted sum of
+the lead fields:
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION is a weight vector
+and INLINE_EQUATION is a vector composed of the
+continuous lead-field functions. The weights are determined by the
+requirement
+
+.. math:: 1 + 1 = 2
+
+i.e., the estimate must predict the measured signals. Hence,
+
+.. math:: 1 + 1 = 2
+
+However, the Gram matrix is ill conditioned and regularization
+must be employed to yield a stable solution. With help of the SVD
+
+.. math:: 1 + 1 = 2
+
+a regularized minimum-norm can now found by replacing the
+data matching condition by
+
+.. math:: 1 + 1 = 2
+
+where
+
+.. math:: 1 + 1 = 2
+
+respectively. In the above, the columns of INLINE_EQUATION are
+the first *k* left singular vectors of INLINE_EQUATION.
+The weights of the regularized estimate are
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION is diagonal with
+
+.. math:: 1 + 1 = 2
+
+INLINE_EQUATION being the INLINE_EQUATION singular
+value of INLINE_EQUATION. The truncation point INLINE_EQUATION is
+selected in mne_analyze by specifying
+a tolerance INLINE_EQUATION, which is used to
+determine INLINE_EQUATION such that
+
+.. math:: 1 + 1 = 2
+
+The extrapolated and interpolated magnetic field or potential
+distribution estimates INLINE_EQUATION in a virtual
+grid of sensors can be now easily computed from the regularized
+minimum-norm estimate. With
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION are the lead fields
+of the virtual sensors,
+
+.. math:: 1 + 1 = 2
+
+Field mapping preferences
+=========================
+
+The parameters of the field maps can be adjusted from the Field mapping preferences dialog shown in :ref:`CACGDCGA` which is accessed through the Adjust/Field mapping... menu item.
+
+.. _CACGDCGA:
+
+.. figure:: picture.png
+ :alt: none
+
+ Field mapping preferences dialog.
+
+The Field mapping preferences dialog
+has the following controls, arranged in MEG , EEG ,
+and common sections:
+
+**SVD truncation at**
+
+ Adjusts the smoothing of the field and potential patterns. This parameter
+ specifies the eigenvalue truncation point as described in :ref:`CACGFBCI`. Smaller values correspond to noisier field
+ patterns with less smoothing.
+
+**Use default origin**
+
+ The location of the origin of the spherical head model used in these computations
+ defaults to (0 0 40) mm. If this box is unchecked the origin coordinate
+ fields are enabled to enter a custom origin location. Usually the
+ default origin is appropriate.
+
+**Downsampling grade**
+
+ This option only applies to EEG potential maps and MEG field maps
+ extrapolated to the head surface and controls the number of virtual
+ electrodes or point magnetometers used in the interpolation. Allowed
+ values are: 2 (162 locations), 3 (642 locations), and 4 (2562 locations).
+ Usually the default value 3 is appropriate.
+
+**Number of smoothsteps**
+
+ This option controls how much smoothing, see Section 8.3,
+ is applied to the interpolated data before computing the contours.
+ Usually the default value is appropriate.
+
+**Reconstruction surface radius**
+
+ Distance of the spherical reconstruction surface from the sphere model
+ origin. Usually default value is appropriate. For children it may
+ be necessary to make this value smaller.
+
+.. _CACBHDBF:
+
+Working with current estimates
+##############################
+
+.. _CACHFFIJ:
+
+Preferences
+===========
+
+The characteristics of the current estimates displayed are
+controlled from the MNE preferences dialog
+which pops up from Adjust/Estimates... .
+
+This dialog, shown in :ref:`CACJGCDH`, has the following
+controls:
+
+**SNR estimate**
+
+ This controls the regularization of the estimate, i.e., the amount
+ of allowed mismatch between the measured data and those predicted by
+ the estimated current distribution. Smaller SNR means larger allowed
+ mismatch. Typical range of SNR values is 1...7. As discussed in Section 6.2,
+ the SNR value can be translated to the current variance values expressed
+ in the source-covariance matrix R. This translation is presented
+ as the equivalent current standard-deviation value
+
+**Show**
+
+ This radio button box selects the quantity to display. MNE is
+ the minimum norm estimate (estimated value of the current), dSPM is the
+ noise-normalized MNE, and sLORETA is
+ another version of the noise-normalized solution which is claimed
+ to have a smaller location bias than the dSPM.
+
+**Mask with**
+
+ If MNE is selected in the Show radio
+ button box, it is possible to mask the solution with one of the
+ statistical maps. The masking map is thresholded at the value given
+ in the Threshold text field and
+ the MNE is only shown in areas with statistical values above this threshold.
+
+**Value histogram**
+
+ This part of the dialog shows the distribution of the currently
+ shown estimate values over the surface. The histogram is colored
+ to reflect the current scale settings. The fthresh , fmid ,
+ and fmax values are indicated
+ with vertical bars. The histogram is updated when the dialog is
+ popped up and when the estimate type to show changes, not at every
+ new time point selection. The Refresh button
+ makes the histogram current at any time.
+
+**Color scale**
+
+ These text fields control the color scale as described in :ref:`CACGGICI`.
+
+**Options**
+
+ Various options controlling the estimates.
+
+.. _CACGGICI:
+
+.. table:: The color scale parameters.
+
+ =========== =======================================================================================================================================================================================================================================================================================
+ Parameter Meaning
+ =========== =======================================================================================================================================================================================================================================================================================
+ fthresh If the value is below this level, it will not be shown.
+ fmid Positive values at this level will show as red. Negative values will be dark blue.
+ fmax Positive values at and above this level will be bright yellow. Negative values will be bright blue.
+ fmult Apply this multiplier to the above thresholds. Default is 1 for statistical maps and INLINE_EQUATION for currents (MNE). The vertical bar locations in the histogram take this multiplier into account but the values indicated are the threshold parameters without the multiplier.
+ tcmult The upper limit of the timecourse vertical scale will be INLINE_EQUATION.
+ =========== =======================================================================================================================================================================================================================================================================================
+
+.. _CACJGCDH:
+
+.. figure:: picture.png
+ :alt: none
+
+ Estimate preferences dialog.
+
+The optional parameters are:
+
+**Retain sign**
+
+ With this option, the sign of the dot product between the current direction
+ and the cortical surface normal will be used as the sign of the
+ values to be displayed. This option yields meaningful data only if
+ a strict or a loose orientation constraint was used in the computation
+ of the inverse operator decomposition.
+
+**Retain normal component only**
+
+ Consider only the current component normal to the cortical mantle. This
+ option is not meaningful with completely free source orientations.
+
+**Show scale bar**
+
+ Show the color scale bar at the lower right corner of the display.
+
+**Show comments**
+
+ Show the standard comments at the lower left corner of the display.
+
+**Time integr. (ms)**
+
+ Integration time for each frame (INLINE_EQUATION).
+ Before computing the estimates time integration will be performed
+ on sensor data. If the time specified for a frame is INLINE_EQUATION,
+ the integration range will be INLINE_EQUATION.
+
+**# of smooth steps**
+
+ Before display, the data will be smoothed using this number of steps,
+ see Section 8.3.
+
+**Opacity**
+
+ The range of this parameter is 0...1. The default value 1 means
+ that the map overlaid on the cortical surface is completely opaque.
+ With lower opacities the color of the cortical surface will be visible
+ to facilitate understanding the underlying folding pattern from
+ the curvature data displayed.
+
+.. _CACJFFEE:
+
+The SNR display
+===============
+
+The SNR estimate display
+shows the SNR estimated from the whitened data in red and the apparent
+SNR inferred from the mismatch between the measured and predicted
+data in green.
+
+The SNR estimate is computed from the whitened data INLINE_EQUATION,
+related to the measured data INLINE_EQUATION by
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION is the whitening
+operator, introduced in Section 6.2.3.
+
+The computation of the apparent SNR will be explained in
+future revisions of this manual.
+
+.. _CACCCFHH:
+
+Inquiring timecourses
+#####################
+
+.. _CHDGHDGE:
+
+Timecourses at vertices
+=======================
+
+Timecourses at individual vertices can be inquired by clicking
+on a desired point on the surface with the left mouse button. If
+the control key was down at the time of a click, the timecourse
+will be added to the timecourse manager but left off. With both
+control and shift down, the timecourse will be added to the timecourse
+manager and switched on. For more information on the timecourse
+manager, see :ref:`CACDIAAD`.
+
+The timecourses are be affected by the Retain sign and Retain normal component only settings in the MNE preferences dialog , see :ref:`CACHFFIJ`.
+
+Timecourses at labels
+=====================
+
+The labels provide means to interrogate timecourse information
+from ROIs. The label files can be created in mne_analyze ,
+see :ref:`CACJCFJJ` or in tksurfer ,
+which is part of the FreeSurfer software. For mne_analyze left-hemisphere
+and right-hemisphere label files should be named <name> ``-lh.label`` and <name> ``-rh.label`` ,
+respectively.
+
+Individual label files can be loaded from Labels/Load label... . All label files in a directory can be
+loaded from Labels/Load all labels... .
+Once labels are loaded, the label list shown in :ref:`CACJJGEF` appears. Each
+time a new label is added to the list, the names will be reordered
+to alphabetical order. This list can be also brought up from Labels/Show label list . The list can be cleared from Labels/Discard all labels .
+
+.. warning:: Because of the format of the label files mne_analyze can not certify that the label files loaded belong to the cortical surfaces of the present subject.
+
+When a label is selected from the label list, the corresponding
+timecourse appears. The Keep button
+stores the timecourse to the timecourse manager, :ref:`CACDIAAD`.
+
+.. _CACJJGEF:
+
+.. figure:: picture.png
+ :alt: none
+
+ The label list.
+
+The timecourse shown in the MNE amplitude window
+is a compound measure of all timecourses within a label. Two measures
+are available:
+
+**Average**
+
+ Compute the average over all label vertices at each time point.
+
+**Maximum**
+
+ Compute the maximum absolute value over all vertices at each time point.
+ If the data are signed, the value is assigned the sign of the value
+ at the maximum vertex. This may make the timecourse jump from positive
+ to negative abruptly if vertices with different signs are included
+ in the label.
+
+**L2 norm (sample by sample)**
+
+ Compute the INLINE_EQUATION norm over the values
+ in the vertices at each time point.
+
+**Pick vertex with largest L2 norm over time**
+
+ Compute the INLINE_EQUATION norm over time in
+ each vertex and show the time course at the vertex with the largest
+ norm.
+
+.. _CACDIAAD:
+
+The timecourse manager
+======================
+
+The timecourse manager shown in :ref:`CACEDEJI` has
+the following controls for each timecourse stored:
+
+.. _CACEDEJI:
+
+.. figure:: picture.png
+ :alt: none
+
+ The timecourse manager.
+
+**Numbered checkbox**
+
+ Switches the display of this timecourse on and off.
+
+**Color...**
+
+ This button shows the color of the timecourse curve. The color can be
+ adjusted from the color editor which appears when the button is pressed.
+
+**Save...**
+
+ Saves the timecourse. If a single vertex is selected, the time course file
+ will contain some comment lines starting with the the percent sign,
+ one row of time point values in seconds and another with the data
+ values. The format of the timecourse data is explained in :ref:`CACJJGFA`, below.
+
+**Forget**
+
+ Delete this timecourse from memory.
+
+.. _CACJJGFA:
+
+Label timecourse files
+----------------------
+
+When timecourse corresponding to a label is saved, the default
+is to save the displayed single timecourse in a format identical
+to the vertex timecourses. If Save all timecourses within the label is selected, the Time-by-time output output changes the output to be listed
+time by time rather than vertex by vertex, Include coordinates adds the vertex location information to
+the output file, and Include vertex numbers adds
+the indices of picked vertices to the output, see :ref:`CACHBBFD`.
+The vertex-by-vertex output formats is summarized in :ref:`CACEFHIJ`.
+
+.. _CACHBBFD:
+
+.. figure:: picture.png
+ :alt: none
+
+ Label timecourse saving options.
+
+.. _CACEFHIJ:
+
+.. table:: Vertex-by-vertex output format. INLINE_EQUATION is the number of vertices, INLINE_EQUATION is the number of time points, INLINE_EQUATION is the number of comment lines, INLINE_EQUATION indicate the times in milliseconds, INLINE_EQUATION is a vertex number, INLINE_EQUATION are the coordinates of vertex INLINE_EQUATION in millimeters, and INLINE_EQUATION are the values at vertex INLINE_EQUATION. Items in brackets are only included if Include coordinates is active. In the time-b [...]
+
+ ================== ======================================================
+ Line Contents
+ ================== ======================================================
+ INLINE_EQUATION Comment lines beginning with %
+ INLINE_EQUATION {0.0 }[0.0 0.0 0.0] INLINE_EQUATION
+ INLINE_EQUATION {INLINE_EQUATION }[INLINE_EQUATION] INLINE_EQUATION
+ ================== ======================================================
+
+.. _CACJCFJJ:
+
+Creating new label files
+========================
+
+It is easy to create new label files in mne_analyze .
+For this purpose, an inflated surface should be visible in the main
+display. Follow these steps:
+
+- Clear all previously selected vertices
+ either by choosing Labels/Clear marked vertices or
+ do a right button click on the surface display with the shift key
+ down.
+
+- Mark vertices on the surface with right button click or by
+ right button drag. The vertices should be defined in the desired
+ order on the new label outline. The outline will follow the shortest
+ path along the surface. The shortest path will be calculated along
+ the white matter surface.Note that sometimes the shortest paths
+ appear to be un-intuitive on the inflated surface.
+
+- Do a right button click with control key down inside the label.
+ The outline will be completed and shown as a yellow line. The inside
+ of the label will be filled and shown in green. A file selection
+ box will appear to save the label. Enter the stem of the file name
+ here. The file name will be augmented with ``-lh.label`` or ``-rh.label`` ,
+ depending on the hemisphere on which the label is specified.
+
+.. _CACFCHEC:
+
+Overlays
+########
+
+.. _CACIGHEJ:
+
+.. figure:: picture.png
+ :alt: none
+
+ The overlay management dialog.
+
+In addition to source estimates derived from MEG and EEG
+data, mne_analyze can be used
+to display other surface-based data. These overlay data can be imported
+from w and stc files containing single time slice (static) and dynamic
+data (movies), respectively. These data files can be produced by mne_make_movie ,
+FreeSurfer software, and custom programs or Matlab scripts.
+
+The names of the files to be imported should end with ``-`` <hemi> .<type> , where <hemi> indicates
+the hemisphere (``lh`` or ``rh`` and <type> is ``w`` or ``stc`` .
+
+Overlays are managed from the dialog shown in :ref:`CACIGHEJ` which is invoked from File/Manage overlays... .
+
+This dialog contains the following
+controls:
+
+**List of overlays loaded**
+
+ Lists the names of the overlays loaded so far.
+
+**Load w...**
+
+ Load a static overlay from a w file. In the open dialog it is possible to
+ specify whether this file contains data for the cortical surface
+ or for scalp. Scalp overlays can be viewed in the viewer window.
+
+**Load stc...**
+
+ Load a dynamic overlay from an stc file. In the open dialog it is
+ possible to specify whether this file contains data for the cortical
+ surface or for scalp. Scalp overlays can be viewed in the viewer window.
+
+**Delete**
+
+ Delete the selected overlay from memory.
+
+**Time scale slider**
+
+ Will be activated if a dynamic overlay is selected. Changes the
+ current time point.
+
+**Overlay type is**
+
+ Selects the type of the data in the current overlay. Different default color
+ scales are provided each overlay type.
+
+**Value histogram**
+
+ Shows the distribution of the values in the current overlay. For
+ large stc files this may take a while to compute since all time
+ points are included. The histogram is colored to reflect the current
+ scale settings. The fthresh , fmid ,
+ and fmax values are indicated
+ with vertical bars.
+
+**Color scale**
+
+ Sets the color scale of the current overlay. To activate the values, press Show .
+ For information on color scale settings, see :ref:`CACGGICI`.
+
+**Options**
+
+ Display options. This a subset of the options in the MNE preferences dialog. For details, see :ref:`CACHFFIJ`.
+
+**Show**
+
+ Show the selected overlay and assign the settings to the current overlay.
+
+**Apply to all**
+
+ Apply the current settings to all loaded overlays.
+
+It is also possible to inquire timecourses of vertices and
+labels from dynamic (stc) cortical overlays in the same way as from
+original data and store the results in text files. If a static overlay
+(w file) or a scalp overlay is selected, the timecourses are picked
+from the data loaded, if available.
+
+.. _CHDGHIJJ:
+
+Fitting current dipoles
+#######################
+
+Starting from MNE software version 2.6, mne_analyze includes
+routines for fitting current dipoles to the data. At present mne_analyze is
+limited to fitting single equivalent current dipole (ECD) at one
+time point. The parameters affecting the dipole fitting procedure
+are described in :ref:`CACEDEGA`. The results are shown in
+the dipole list (:ref:`CACGGAIA`). The selection of channels
+included can be adjusted interactively or by predefined selections
+as described in :ref:`CACIBHCI`.
+
+.. warning:: The current dipole fitting has been added recently and has not been tested comprehensively. Especially fitting dipoles to EEG data may be unreliable.
+
+.. _CACEDEGA:
+
+Dipole fitting parameters
+=========================
+
+Prior to fitting current dipoles, the fitting parameters
+must be set with the Dipole fitting preferences dialog
+shown in :ref:`CACFEDEJ`. The dialog is brought up from the Setup fitting... choice in the Dipoles menu.
+This dialog contains three sections: Forward model , Modalities ,
+and Noise estimate .
+
+The Forward model section
+specifies the forward model to be used:
+
+**Sphere model origin x/y/z\m]**
+
+ Specifies the origin of the spherically symmetric conductor model in
+ MEG/EEG head coordinates, see Section 5.3.
+
+**EEG scalp radius\m]**
+
+ Specifies the radius of the outermost shell in the EEG sphere model. For
+ details, see Section 5.9.4.
+
+**EEG sphere model name**
+
+ Specifies the name of the EEG sphere model to use. For details,
+ see Section 5.9.4.
+
+**BEM model**
+
+ Selects the boundary-element model to use. The button labeled with ... brings
+ up a file-selection dialog to select the BEM file. An existing selection
+ can be cleared with the Unset button.
+ If EEG data are included in fitting, this must be a three-compartment
+ model. Note that the sphere model is used even with a BEM model
+ in effect, see :ref:`CHDFGIEI`.
+
+**Accurate field calculation**
+
+ Switches on the more accurate geometry definition of MEG coils, see Section 5.8.
+ In dipole fitting, there is very little difference between the *accurate* and *normal* coil
+ geometry definitions.
+
+The Modalities section
+defines which kind of data (MEG/EEG) are used in fitting. If an
+inverse operator is loaded with the data, this section is fixed and
+greyed out. You can further restrict the selection of channels used
+in dipole fitting with help of channel selections discussed in :ref:`CACIBHCI`.
+
+The Noise estimate section
+of the dialog contains the following items:
+
+**Noise covariance**
+
+ Selects the file containing the noise-covariance matrix. If an inverse operator
+ is loaded, the default is the inverse operator file. The button labeled
+ with ... brings up a file-selection
+ dialog to select the noise covariance matrix file. An existing selection
+ can be cleared with the Unset button.
+
+**Omit off-diagonal terms**
+
+ If a noise covariance matrix is selected, this choice omits the
+ off-diagonal terms from it. This means that individual noise estimates for
+ each channel are used but correlations among channels are not taken
+ into account.
+
+**Regularization**
+
+ Regularize the noise covariance before using it in whitening by
+ adding a multiple of an identity matrix to the diagonal. This is
+ discussed in more detail in Section 6.2.4. Especially if
+ EEG is included in fitting it is advisable to enter a non-zero value
+ (around 0.1) here.
+
+**Planar fixed\T/cm]**
+
+ In the absense of a noise covariance matrix selection, a diagonal noise
+ covariance with fixed values on the diagonal is used. This entry
+ specifies the fixed value of the planar gradiometers.
+
+**Axial fixed\T]**
+
+ If a noise covariance matrix file is not specified, this entry specifies a
+ fixed diagonal noise covariance matrix value for axial gradiometers
+ and magnetometers.
+
+**EEG fixed [INLINE_EQUATIONV]**
+
+ If a noise covariance matrix file is not specified, this entry specifies a
+ fixed diagonal noise covariance matrix value for axial gradiometers
+ and magnetometers..
+
+.. _CACFEDEJ:
+
+.. figure:: picture.png
+ :alt: none
+
+ The dipole fitting preferences dialog.
+
+.. _CHDFGIEI:
+
+The dipole fitting algorithm
+============================
+
+When the dipole fitting preferences dialog is closed and
+the values have been modified the following preparatory calculations
+take place:
+
+- If EEG data are included in fitting
+ present, the EEG sphere model specification corresponding to EEG sphere model name is loaded and scaled to the
+ the EEG scalp radius .
+
+- If a boundary-element model is used, the additional data depending
+ on the sensor locations are computed.
+
+- The noise covariance matrix is composed according to the specifications
+ in the Dipole fitting preferences dialog.
+
+- The spatially whitened forward solution is computed in a grid
+ of locations to establish the initial guess when a dipole is fitted.
+ If a BEM is in use, the grid will be confined to the inner skull
+ volume. For a sphere model, a spherical volume with an 80-mm radius,
+ centered at the sphere model origin, will be employed. The dipole
+ grid will be rectangular with a 10-mm spacing between the closest
+ dipole locations. Any locations closer than 20 mm to the center
+ of mass of the grid volume will be excluded as well as those closer
+ than 10 mm to the surface. Note that this guess grid is only used
+ for establishing the initial guess; the actual dipole fitting procedure
+ does not constrain the solution to this grid.
+
+When the Fit ECD button
+in the tool bar is clicked with a time point selected from the the
+response, the optimal Equivalent Current Dipole parameters (location,
+orientation, and amplitude) are determined using the following algorithm:
+
+- An initial guess for the location of
+ the dipole is determined using the grid of locations determined
+ in step 4., above. At each guess dipole location, the least squares
+ error between the measured data and a dipole at that location is
+ evaluated and the location corresponding to the smallest error is
+ used as the initial guess location. In this process, the dipole
+ amplitude parameters do not need to be explicitly calculated.
+
+- Using the Nelder-Mead simplex optimization algorithm, an optimal dipole
+ location is determined with the sphere model used as the forward
+ model. Again, the dipole amplitude parameters are not explicitly present
+ in the fitting procedure.
+
+- A second optimization interation using the boundary-element
+ model (if available) or the sphere model as the forward model is
+ conducted. The reason for repeating the optimization even with the
+ sphere model is to reduce the likelihood of having been stuck in
+ a local minimum of the least squares error criterion.
+
+- The optimal dipole amplitude parameters are determined for
+ the optimal dipole location obtained in steps 2. and 3.
+
+- The dipole parameters are reported in the dipole list discussed
+ in :ref:`CACGGAIA`.
+
+Additional notes:
+
+- The noise covariance matrix is always
+ applied to the data and the forward solution as appropriate to correctly
+ weight the different types of MEG channels and EEG. Depending on
+ the dipole fitting settings, the noise covariance may be either
+ a diagonal matrix or a full matrix including the correlations.
+
+- Using the SVD of the whitened gain matrix of three dipole
+ componets at a given location, the component producing the weakest
+ signal amplitude is omitted if the ratio of the smallest and largest
+ singular values is less than 0.2.
+
+- The present MNE software package also contains a batch-mode
+ dipole fitting program called mne_dipole_fit .
+ This piece of software is not yet documented here. However, ``mne_dipole_fit --help`` lists the command-line options which have direct correspondence
+ to the interactive dipole fitting options discussed here.
+
+.. _CACGGAIA:
+
+The dipole list
+===============
+
+.. _CACGGFEJ:
+
+.. figure:: picture.png
+ :alt: none
+
+ The dipole list.
+
+The dipole list dialog shown in :ref:`CACGGFEJ` contains
+the parameters of the dipoles fitted. In addition, it is possible
+to import current dipole locations from the Neuromag source modelling
+program xfit to mne_analyze . Dipoles
+can be imported in two ways:
+
+- Bring up the dipole list window from Windows/Show dipole list... . Drag and drop selected dipoles
+ from one of the xfit dipole list
+ to this list using the middle mouse button.
+
+- Drag and drop dipoles from one of the xfit dipole
+ lists over the main surface display. The dipole list will appear
+ and contain the dropped dipoles.
+
+The buttons at the bottom of the dialog perform the following
+functions:
+
+**Done**
+
+ Hide
+ the dialog.
+
+**Show**
+
+ Show
+ the currently selected dipoles as specified in Display options ,
+ see below.
+
+**Save**
+
+ Save the selected (or all) dipoles.
+ If the file name specified in the file selection dialog that pops
+ up ends with ``.bdip`` , the dipole data will be saved in
+ the binary bdip format compatible with
+ the Neuromag xfit software, otherwise,
+ a text format output will be used. In the text file, comments will
+ be included on lines starting with the percent sign so that the
+ text format can be easily loaded into Matlab.
+
+**Clear**
+
+ Clear
+ the selected dipoles from the list.
+
+When you double click on one of the dipoles or select several
+dipoles and click Show points
+on the surface displayed in the vicinity of the dipoles will be
+painted according to the specifications given in the Options section of
+the dialog:
+
+**Color**
+
+ By the default, the dipoles are marked in green with transparency (alpha)
+ set to 0.5. I you click on one of the dipoles, you can adjust the
+ color of this dipole by editing the color values or from the color editor
+ appearing when you click Color... .
+ When you click Apply , the new
+ color values are attached to the selected dipole.
+
+**Max. distance for dipoles to show (mm)**
+
+ If this option is on, only dipoles which are closer to the surface
+ than the distance specified in the adjacent text field are displayed.
+
+**Paint all point closer than (mm)**
+
+ Instead of indicating the point closest to the dipole all points
+ closer than the distance given in the text field will be painted
+ if this option is on. This choice is useful for understanding the
+ shape of the neighborhood of a dipole on the cortical surface.
+
+**Number of smooth steps**
+
+ This option spreads out the dipole marking by the given number of smooth
+ steps to make the dipoles more clearly visible. A suitable choice
+ is 3 or 4.
+
+**Keep previous dipoles**
+
+ If this option is on, previously marked dipoles are not cleared
+ from the display before new ones are shown.
+
+.. note:: The surface must be loaded to display dipole locations. To calculate the distance from the dipoles to the white matter surface, the white matter tessellation is loaded as needed. Depending on the precise location of the fitted dipole, the spot indicating the dipole site may easily appear on a different wall of a fissure than could be expected. The fissural walls can be far apart from each other in the inflated view of the cortex even if they are physically [...]
+
+.. _CACIBHCI:
+
+Channel selections
+==================
+
+As mentioned in :ref:`CACHBJAC`, the right mouse button
+in the topographical display of channels can be used to restrict
+the selection of channels taken into account in dipole fitting.
+In addition, the channel selections can be manipulated in the channel
+selection window, which pops up from Dipoles/Manage channel selections... . Initially this dialog contains
+the selections defined in or $HOME/.mne/mne_analyze.sel or $MNE_ROOT/share/mne/mne_analyze/mne_analyze.sel,
+the personal file taking precedence over the system wide default.
+The Save button in this dialog
+save the current set of channel selections to the personal selection
+file. The format of this file is identical to the channel selection
+file in mne_browse_raw .
+
+When a channel selection file is in effect. the variances
+of the unselected channels are increased by a factor of 900. This
+means that unselected channels receive virtually no weight in the
+least-squares error function or, equivalently, that they are considered
+to be 30 times more noisy than their true noise value. Since this
+implementation of channel selections requires recomputation of the
+initial guess candidate data discussed in :ref:`CHDFGIEI`,
+above, changing the selection may take a finite amount of time,
+especially if a BEM is used for the forward calculation.
+
+.. note:: Please note that when making a channel selection in the topographical displays, the channels not present in a particular layout are also affected. For example, if you select channels in a layout showing the Vectorview planar gradiometers, the magnetometer channels and EEG channels will be unselected.
+
+.. _CACEHGCD:
+
+Coordinate frame alignment
+##########################
+
+The MRI-MEG coordinate frame alignment tools included in mne_analyze utilized
+the 3D digitizer (Polhemus) data acquired in the beginning of each
+MEG/EEG session and the scalp surface triangulation shown in the
+viewer window. To access the coordinate frame alignment tools:
+
+- Load digitizer data. You can either
+ load a data set containing digitizer information or load digitizer
+ data from a file through the File/Load digitizer data... menu choice.
+
+- Set up the viewer window and make it visible, see :ref:`CACEFFJF`. The viewer options should be set to show the
+ digitizer data, see :ref:`CACHGDEA`.
+
+- Bring up the Adjust coordinate alignment dialog from Adjust/Coordinate alignment... .
+
+.. figure:: picture.png
+ :alt: none
+
+ The coordinate frame alignment dialog.
+
+The coordinate frame alignment dialog contains the following
+sections:
+
+- Buttons for picking the fiducial points
+ from the scalp surface and one for setting an initial alignment
+ using these points. When one of the fiducials is selected, the viewer
+ display automatically rotates to a suitable orientation to make
+ the corresponding fiducial accessible.
+
+- Controls for fine tuning the alignment. These include movements
+ along the three orthogonal coordinate axes and rotations around
+ them. The buttons marked L and R indicate
+ rotations in counterclockwise and clockwise directions, respectively.
+ The amount of movement (mm) or rotation (degrees) is given in the
+ text fields next to the adjustment buttons.
+
+- Access to an automatic alignment procedure, which employs
+ the Iterative Closest Point (ICP) algorithm.
+
+- Listing of the current coordinate transformation.
+
+- Buttons for discarding outlier points (Discard... ), and for
+ saving and loading the coordinate transformation.
+
+The saving and loading choices are:
+
+**Save default**
+
+ Saves a file which contains the MEG/MRI coordinate transformation
+ only. The file name is generated from the name of the file from which
+ the digitization data were loaded by replacing the ending ``.fif`` with ``-trans.fif`` .
+ If this file already exists, it will be overwritten without any
+ questions asked.
+
+**Save MRI set**
+
+ This option searches for a file called COR.fif in $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets.
+ The file is copied to COR-<username>-<date>-<time>.fif
+ and the current MEG/MRI coordinate transformation as well as the
+ fiducial locations in MRI coordinates are inserted.
+
+**Save...**
+
+ Saves a file which contains the MEG/MRI coordinate transformation
+ only. The ending ``-trans.fif`` is recommended. The file name
+ selection dialog as a button to overwrite.
+
+**Load...**
+
+ Loads the MEG/MRI coordinate transformation from the file specified.
+
+The MEG/MRI coordinate transformation files are employed
+in the forward calculations. The convenience script mne_do_forward solution described in Section 3.11 uses
+a search sequence which is compatible with the file naming conventions
+described above. It is recommended that -trans.fif file
+saved with the Save default and Save... options
+in the mne_analyze alignment
+dialog are used because then the $SUBJECTS_DIR/$SUBJECT directory
+will be composed of files which are dependent on the subjects's
+anatomy only, not on the MEG/EEG data to be analyzed.
+
+Each iteration step of the Iterative Closest Point (ICP) algorithm consists of
+two matching procedures:
+
+- For each digitizer point, transformed
+ from MEG to the MRI coordinate frame using the current coordinate
+ transformation, the closest point on the triangulated surface is
+ determined.
+
+- The best coordinate transformation aligning the digitizer
+ points with the closest points on the head surface is computed.
+
+These two steps are iterated the designated number of times.
+If the Try to keep nasion in place option
+is on, the present location of the nasion receives a strong weight
+in the second part of each iteration step so that nasion movements
+are discouraged.
+
+.. note:: One possible practical approach to coordinate frame alignment is discussed in Section 12.11.
+
+.. _CHDCGHIF:
+
+Using a high-resolution head surface tessellations
+==================================================
+
+The newest version of FreeSurfer contains a script called mkheadsurf which
+can be used for coordinate alignment purposes. For more information,
+try ``mkheadsurf --help`` . This script produces a file
+called ``surf/lh.smseghead`` , which can be converted into
+a fif file using mne_surf2bem.
+
+Suggested usage:
+
+- Set the SUBJECTS_DIR correctly.
+
+- Run mkheadsurf: ``mkheadsurf -subjid`` <subject> .
+
+- Goto the directory ``$SUBJECTS_DIR/`` <subject> ``/bem`` .
+
+- Convert the head surface file: ``mne_surf2bem --surf ../surf/lh.smseghead --id 4 --check --fif`` <subject> ``-head-dense.fif``
+
+- Rename the existing head surface file to <subject> ``-head-sparse.fif``
+
+- Copy <subject> ``-head-dense.fif`` to <subject> ``-head.fif``
+
+- Click Reload in the viewer
+ window.
+
+After this you can switch between the dense and smooth head
+surface tessellations by copying either <subject> ``-head-dense.fif`` or <subject> ``-head-sparse.fif`` to <subject> ``-head.fif`` .
+
+If you have Matlab software available on your system, you
+can also benefit from the script mne_make_scalp_surfaces .
+This script invokes mkheadsurf and
+subsequently decimates it using the mne_reduce_surface function
+in the MNE Matlab toolbox, which in turn invokes the reducepatch
+Matlab function. As a result, the $SUBJECTS_DIR/$SUBJECT/bem directory
+will contain 'dense', 'medium',
+and 'sparse' scalp surface tessellations. The
+dense tessellation contains the output of mkheadsurf while
+the medium and sparse tessellations comprise 30,000 and 2,500 triangles,
+respectively. You can then make a symbolic link of one of these
+to <subject> ``-head.fif`` .
+The medium grade tessellation is an excellent compromize between
+geometric accuracy and speed in the coordinate system alignment.
+
+.. note:: While the dense head surface tessellation may help in coordinate frame alignment, it will slow down the operation of the viewer window considerably. Furthermore, it cannot be used in forward modelling due to the huge number of triangles. For the BEM, the dense tessellation does not provide much benefit because the potential distributions are quite smooth and widespread on the scalp.
+
+.. _CACJJBGF:
+
+Using fiducial points identified by other software
+==================================================
+
+If you have identified the three fiducial points in software
+outside mne_analyze , it is possible
+to display this information on the head surface visualization. To
+do this, you need to copy the file containing the fiducial location
+information in MRI (surface RAS) coordinates to $SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-fiducials.fif.
+There a three supported ways to create this file:
+
+- Use the mne_make_fiducial_file.m Matlab
+ function (not yet written) to create this file.
+
+- Copy a MRI description file with the MEG-MRI coordinate transformation
+ created with MRIlab (typically $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets/COR-<date>.fif
+ to $SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-fiducials.fif.
+
+- For the average subject, fsaverage ,
+ copy the fsaverage-fiducials.fif file provided with mne_analyze
+ in place, see :ref:`CACGEAFI`.
+
+.. _CACIADAI:
+
+Viewing continuous HPI data
+###########################
+
+.. _CACFHFGJ:
+
+.. figure:: picture.png
+ :alt: none
+
+ Continuous HPI data overview.
+
+The newest versions of Neuromag software allow continuous
+acquisition of signals from the HPI coils. On the basis of these
+data the relative position of the dewar and the head can be computed
+a few times per second. The resulting location data, expressed in
+the form of unit quaternions (see http://mathworld.wolfram.com/Quaternion.html)
+and a translation.
+
+The continuous HPI data can be through the File/View continuous HPI data... menu item, which pops up
+a standard file selection dialog. If the file specified ends with ``.fif`` a
+fif file containing the continuous coordinate transformation information
+is expected. Otherwise, a text log file is read. Both files are
+produced by the Neuromag maxfilter software.
+
+Once the data have been successfully loaded, the dialog shown
+in :ref:`CACFHFGJ` appears. It contains the following information:
+
+- Currently selected time point and overview
+ of the data at the current time point,
+
+- MEG device to MEG head coordinate transformation at the current time
+ point and the incremental transformation from the initial timepoint
+ to the current file.
+
+- Graphical display of the data.
+
+- Controls for the graphical display.
+
+The overview items are:
+
+**GOF**
+
+ Geometric mean of the goodness of fit values of the HPI coils at
+ this time point.
+
+**Origin movement**
+
+ The distance between the head coordinate origins at the first and current
+ time points.
+
+**Angular velocity**
+
+ Estimated current angular velocity of the head.
+
+**Coil movements**
+
+ Comparison of the sensor locations between the first and current time
+ points. The minimum, maximum, average, and median sensor movements
+ are listed.
+
+The graphical display contains the following data:
+
+- The geometric mean of the HPI coil goodness
+ of fits (red curve). The scale for this curve is always 0.9...1.0.
+
+- The average coil (sensor) movement value (blue curve). The
+ scale is adjustable from the buttons below the display.
+
+- The estimated angular velocity (deg/s, green curve). The scale
+ is adjustable from the buttons below the display.
+
+- The current time point indicated with a black cursor.
+
+The slider below the display can be used to select the time
+point. If you click on the slider, the current time can be adjusted
+with the arrow keys. The current head position with respect to the
+sensor array is show in the viewer window if it is visible, see :ref:`CACEFFJF`. Note that a complete set of items listed above
+is only available if a data file has been previously loaded, see :ref:`CACBACHB`.
+
+.. _CACCHCBF:
+
+Working with the MRI viewer
+###########################
+
+.. _CHDEGEHE:
+
+.. figure:: picture.png
+ :alt: none
+
+ The MRI viewer control window.
+
+Selecting Show MRI viewer... from
+the View menu starts the FreeSurfer MRI
+viewer program tkmedit to work
+in conjunction with mne_analyze . After
+a few moments, both tkmedit with
+the current subject's T1 MRI data shown and the MRI viewer
+control window shown in :ref:`CHDEGEHE` appear. Note that
+the tkmedit user interface is
+initially hidden. The surfaces of a subject must be loaded before
+starting the MRI viewer.
+
+The MRI viewer control window contains
+the following items:
+
+**Show MRI viewer user interface**
+
+ If this item is checked, the tkmedit user
+ interface window will be show.
+
+**Track surface location in MRI**
+
+ With this item checked, the cursor in the MRI data window follows the
+ current (clicked) location in surface display or viewer. Note that for
+ the *viewer* window the surface location will
+ inquired from the surface closest to the viewer. The MEG helmet
+ surface will not be considered. For example, if you click at an
+ EEG electrode location with the scalp surface displayed, the location
+ of that electrode on the scalp will be shown. The cortical surface
+ locations are inquired from the white matter surface.
+
+**Show dipole locations in MRI**
+
+ If this option is selected, whenever a dipole is displayed in the
+ surface view using the dipole list dialog discussed in :ref:`CACGGAIA` the cursor will also move to the same location
+ in the MRI data window.
+
+**Show digitizer data in MRI**
+
+ If digitizer data are loaded, this option shows the locations with green
+ diamonds in the MRI data.
+
+**Interpolate voxels**
+
+ Toggles trilinear interpolation in the MRI data on and off.
+
+**Max. intensity projection**
+
+ Shows a maximum-intensity projection of the MRI data. This is useful
+ in conjunction with the Show digitizer data in MRI option to evaluate the MEG/MRI coordinate
+ alignment
+
+**Recenter MRI display**
+
+ Brings the cursor to the center of the MRI data.
+
+**Show surface data in MRI**
+
+ This button creates an MRI data set containing the surface data
+ displayed and overlays in with the MRI slices shown in the MRI viewer.
+
+**Show segmentation data in MRI**
+
+ If available, the standard automatically generated segmentation
+ volume (mri/aparc+aseg) is overlaid on the MRI using the standard FreeSurfer
+ color lookup table ($FREESURFER_HOME/FreeSurferColorLUT.txt). As
+ a result, the name of the brain structure or region of corex at
+ the current location of the cursor will be reported if the tkmedit user
+ interface is visible. After the segmentation is loaded this button
+ toggles the display of the segmentation on and off.
+
+**Show command input and output**
+
+ Allows sending tcl commands to tkmedit and
+ shows the responses received. The tkmedit tcl scripting
+ commands are discussed at https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting.
+
+.. _CACGEAFI:
+
+Working with the average brain
+##############################
+
+The FreeSurfer software includes an average subject (fsaverage)
+with a cortical surface reconstruction. In some cases, the average
+subject can be used as a surrogate if the MRIs of a subject are
+not available.
+
+The MNE software comes with additional files which facilitate
+the use of the average subject in conjunction with mne_analyze .
+These files are located in the directory $MNE_ROOT/mne/setup/mne_analyze/fsaverage:
+
+**fsaverage_head.fif**
+
+ The approximate head surface triangulation for fsaverage.
+
+**fsaverage_inner_skull-bem.fif**
+
+ The approximate inner skull surface for fsaverage.
+
+**fsaverage-fiducials.fif**
+
+ The locations of the fiducial points (LPA, RPA, and nasion) in MRI coordinates,
+ see :ref:`CACJJBGF`.
+
+**fsaverage-trans.fif**
+
+ Contains a default MEG-MRI coordinate transformation suitable for fsaverage.
+ For details of using the default transformation, see :ref:`CACBACHB`.
+
+.. _CACJEFAI:
+
+Compatibility with cliplab
+##########################
+
+The following graphics displays are compatible with the Elekta-Neuromag
+report composer cliplab :
+
+- The main surface display area in the
+ main window, see :ref:`CACFJICC`.
+
+- The viewer, see :ref:`CACEFFJF`.
+
+- The sample channel display, see :ref:`CACFGHBJ`.
+
+- The topographical data display, see :ref:`CACHBJAC`.
+
+- The SNR time course display, see :ref:`CACJFFEE`.
+
+- The source time course display, see:ref:`CACCCFHH`
+
+The graphics can be dragged and dropped from these windows
+to one of the cliplab view areas
+using the middle mouse button. Because the topographical display
+area has another function (bed channel selection) tied to the middle
+mouse button, the graphics is transferred by doing a middle mouse
+button drag and drop from the label showing the current time underneath
+the display area itself.
+
+.. note:: The cliplab drag-and-drop functionality requires that you have the proprietary Elekta-Neuromag analysis software installed. mne_analyze is compatible with cliplab versions 1.2.13 and later.
+
+.. _CHDEDFAE:
+
+Visualizing the head position
+#############################
+
+When mne_analyze is invoked
+with the --visualizehpi option, a simplified user interface shown
+in :ref:`CHDJJGII` is displayed. This interface consists only
+of the viewer window. This *head position visualization* mode
+can be used with existing data files but is most useful for showing
+immediate feedback of the head position during experiments with
+an Elekta-Neuromag MEG system.
+
+.. _CHDJJGII:
+
+.. figure:: picture.png
+ :alt: none
+
+ Snapshot of mne_analyze in the head position visualization mode.
+
+As described in :ref:`CHDJECCG`, the head position
+visualization mode can be customized with the --dig, --hpi, --scalehead,
+and --rthelmet options. For this mode to be useful, the --dig and
+--hpi options are mandatory. If existing saved data are viewed,
+both of these can point to a average or raw data file. For on-line
+operation with the Elekta-Neuromag systems, the following files
+in should be used:
+
+``--dig /neuro/dacq/meas_info/isotrak --hpi /neuro/dacq/meas_info/hpi_result``
+
+.. note:: Since MNE software runs only on LINUX and Mac OS X platforms, one usually needs to NFS mount the volume containing /neuro directory to another system and access these files remotely. However, Neuromag has indicated that future versions of their acquisition software will run on the LINUX platform as well and the complication of remote operation can then be avoided.
+
+When mne_analyze starts
+in the head position visualization mode and the --dig and --hpi
+options have been specified, the following sequence operations takes
+place:
+
+- The digitizer data, the coordinate transformation
+ between the MEG device and head coordinate frames, as well as the
+ average head surface provided with the MNE software are loaded.
+
+- If the --scalehead option is invoked, the average head surface
+ is scaled to the approximate size of the subject's head
+ by fitting a sphere to the digitizer and to the head surface points
+ lying above the plane of the fiducial landmarks, respectively. The
+ standard head surface is then scaled by the ration of the radiuses
+ of these two best-fitting spheres. Without --scalehead, the standard
+ head surface is used as is without scaling.
+
+- The known positions of (scaled) fiducial landmarks are matched
+ with those available in the digitizer data. This initial alignment
+ is then refined using the ICP algorithm, see :ref:`CACEHGCD`.
+ This automatic procedure is found to be accurate enough for the
+ visualization purposes.
+
+- Using the coordinate transformation thus established between
+ the coordinate system of the scalp surface (MRI coordinates) and
+ the MEG head coordinates together with the coordinate transformation
+ between the MEG head and device coordinate frames established with
+ HPI, the position of the MEG helmet surface is shown in the viewer
+ window.
+
+If the --rthelmet option was present, the room-temperature
+helmet surface is shown instead of the MEG sensor surface. The digitizer
+and HPI data files are reloaded and the above steps 1. - 4. are
+repeated when the Reload HPI button
+is pressed. The comment lines in the viewer window show information
+about the digitizer and HPI data files as well as the location of the
+MEG device coordinate origin in the MEG head coordinate system.
+
+.. note:: The appearance of the viewer visualization can be customized using the Options... button, see :ref:`CACHGDEA`. Since only the scalp and MEG device surfaces are loaded, only a limited number of options is active. The display can also be saved as an image from the img button, see :ref:`CACBEBGC`.
diff --git a/doc/source/manual/browse.rst b/doc/source/manual/browse.rst
new file mode 100644
index 0000000..64d6f5e
--- /dev/null
+++ b/doc/source/manual/browse.rst
@@ -0,0 +1,2605 @@
+
+
+.. _CACCICGI:
+
+===================
+Processing raw data
+===================
+
+Overview
+########
+
+The raw data processor mne_browse_raw is
+designed for simple raw data viewing and processing operations. In
+addition, the program is capable of off-line averaging and estimation
+of covariance matrices. mne_browse_raw can
+be also used to view averaged data in the topographical layout.
+Finally, mne_browse_raw can communicate
+with mne_analyze described in Chapter 7 to
+calculate current estimates from raw data interactively.
+
+mne_browse_raw has also
+an alias, mne_process_raw . If mne_process_raw is
+invoked, no user interface appears. Instead, command line options
+are used to specify the filtering parameters as well as averaging
+and covariance-matrix estimation command files for batch processing. This
+chapter discusses both mne_browse_raw and mne_process_raw .
+
+.. _CACHCFEG:
+
+Command-line options
+####################
+
+This section first describes the options common to mne_browse_raw and mne_process_raw .
+Thereafter, options unique to the interactive (mne_browse_raw )
+and batch (mne_process_raw ) modes are
+listed.
+
+.. _BABBGJEA:
+
+Common options
+==============
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---cd <dir>**
+
+ Change to this directory before starting.
+
+**\---raw <name>**
+
+ Specifies the raw data file to be opened. This option is required
+ for batch version, mne_process_raw. If
+ a raw data file is not specified for the interactive version, mne_browse_raw ,
+ and empty interactive browser will open.
+
+**\---grad <number>**
+
+ Apply software gradient compensation of the given order to the data loaded
+ with the ``--raw`` option. This option is effective only
+ for data acquired with the CTF and 4D Magnes MEG systems. If orders
+ different from zero are requested for Neuromag data, an error message appears
+ and data are not loaded. Any compensation already existing in the
+ file can be undone or changed to another order by using an appropriate ``--grad`` options.
+ Possible orders are 0 (No compensation), 1 - 3 (CTF data), and 101
+ (Magnes data). The same compensation will be applied to all data
+ files loaded by mne_process_raw . For mne_browse_raw ,
+ this applies only to the data file loaded by specifying the ``--raw`` option.
+ For interactive data loading, the software gradient compensation
+ is specified in the corresponding file selection dialog, see :ref:`CACDCHAJ`.
+
+**\---filtersize <size>**
+
+ Adjust the length of the FFT to be applied in filtering. The number will
+ be rounded up to the next power of two. If the size is INLINE_EQUATION,
+ the corresponding length of time is INLINE_EQUATION,
+ where INLINE_EQUATION is the sampling frequency
+ of your data. The filtering procedure includes overlapping tapers
+ of length INLINE_EQUATION so that the total FFT
+ length will actually be INLINE_EQUATION. This
+ value cannot be changed after the program has been started.
+
+**\---highpass <value/Hz>**
+
+ Highpass filter frequency limit. If this is too low with respect
+ to the selected FFT length and, the data will not be highpass filtered. It
+ is best to experiment with the interactive version to find the lowest applicable
+ filter for your data. This value can be adjusted in the interactive
+ version of the program. The default is 0, *i.e.*,
+ no highpass filter apart from that used during the acquisition will
+ be in effect.
+
+**\---highpassw <value/Hz>**
+
+ The width of the transition band of the highpass filter. The default
+ is 6 frequency bins, where one bin is INLINE_EQUATION. This
+ value cannot be adjusted in the interactive version of the program.
+
+**\---lowpass <value/Hz>**
+
+ Lowpass filter frequency limit. This value can be adjusted in the interactive
+ version of the program. The default is 40 Hz.
+
+**\---lowpassw <value/Hz>**
+
+ The width of the transition band of the lowpass filter. This value
+ can be adjusted in the interactive version of the program. The default
+ is 5 Hz.
+
+**\---eoghighpass <value/Hz>**
+
+ Highpass filter frequency limit for EOG. If this is too low with respect
+ to the selected FFT length and, the data will not be highpass filtered.
+ It is best to experiment with the interactive version to find the
+ lowest applicable filter for your data. This value can be adjusted in
+ the interactive version of the program. The default is 0, *i.e.*,
+ no highpass filter apart from that used during the acquisition will
+ be in effect.
+
+**\---eoghighpassw <value/Hz>**
+
+ The width of the transition band of the EOG highpass filter. The default
+ is 6 frequency bins, where one bin is INLINE_EQUATION.
+ This value cannot be adjusted in the interactive version of the
+ program.
+
+**\---eoglowpass <value/Hz>**
+
+ Lowpass filter frequency limit for EOG. This value can be adjusted in
+ the interactive version of the program. The default is 40 Hz.
+
+**\---eoglowpassw <value/Hz>**
+
+ The width of the transition band of the EOG lowpass filter. This value
+ can be adjusted in the interactive version of the program. The default
+ is 5 Hz.
+
+**\---filteroff**
+
+ Do not filter the data. This initial value can be changed in the
+ interactive version of the program.
+
+**\---digtrig <name>**
+
+ Name of the composite digital trigger channel. The default value
+ is 'STI 014'. Underscores in the channel name
+ will be replaced by spaces.
+
+**\---digtrigmask <number>**
+
+ Mask to be applied to the trigger channel values before considering them.
+ This option is useful if one wants to set some bits in a don't care
+ state. For example, some finger response pads keep the trigger lines
+ high if not in use, *i.e.*, a finger is not in
+ place. Yet, it is convenient to keep these devices permanently connected
+ to the acquisition system. The number can be given in decimal or
+ hexadecimal format (beginning with 0x or 0X). For example, the value
+ 255 (0xFF) means that only the lowest order byte (usually trigger
+ lines 1 - 8 or bits 0 - 7) will be considered.
+
+.. note:: Multiple raw data files can be specified for mne_process_raw .
+
+.. note:: Strictly speaking, trigger mask value zero would mean that all trigger inputs are ignored. However, for convenience, setting the mask to zero or not setting it at all has the same effect as 0xFFFFFFFF, *i.e.*, all bits set.
+
+.. note:: The digital trigger channel can also be set with the MNE_TRIGGER_CH_NAME environment variable. Underscores in the variable value will *not* be replaced with spaces by mne_browse_raw or mne_process_raw . Using the ``--digtrig`` option supersedes the MNE_TRIGGER_CH_NAME environment variable.
+
+.. note:: The digital trigger channel mask can also be set with the MNE_TRIGGER_CH_MASK environment variable. Using the ``--digtrigmask`` option supersedes the MNE_TRIGGER_CH_MASK environment variable.
+
+.. _CACCHAGA:
+
+Interactive mode options
+========================
+
+These options apply to the interactive (mne_browse_raw )
+version only.
+
+**\---allowmaxshield**
+
+ Allow loading of unprocessed Elekta-Neuromag data with MaxShield
+ on. These kind of data should never be used for source localization
+ without further processing with Elekta-Neuromag software.
+
+**\---deriv <name>**
+
+ Specifies the name of a derivation file. This overrides the use
+ of a standard derivation file, see :ref:`CACFHAFH`.
+
+**\---sel <name>**
+
+ Specifies the channel selection file to be used. This overrides
+ the use of the standard channel selection files, see :ref:`CACCJEJD`.
+
+.. _CACFAAAJ:
+
+Batch-mode options
+==================
+
+These options apply to the batch-mode version, mne_process_raw only.
+
+**\---proj <name>**
+
+ Specify the name of the file of the file containing a signal-space
+ projection (SSP) operator. If ``--proj`` options are present
+ the data file is not consulted for an SSP operator. The operator
+ corresponding to average EEG reference is always added if EEG data
+ are present.
+
+**\---projon**
+
+ Activate the projections loaded. One of the options ``--projon`` or ``--projoff`` must
+ be present on the mne_processs_raw command line.
+
+**\---projoff**
+
+ Deactivate the projections loaded. One of the options ``--projon`` or ``--projoff`` must
+ be present on the mne_processs_raw command line.
+
+**\---makeproj**
+
+ Estimate the noise subspace from the data and create a new signal-space
+ projection operator instead of using one attached to the data file
+ or those specified with the ``--proj`` option. The following
+ eight options define the parameters of the noise subspace estimation. More
+ information on the signal-space projection can be found in :ref:`CACCHABI`.
+
+**\---projevent <no>**
+
+ Specifies the events which identify the time points of interest
+ for projector calculation. When this option is present, ``--projtmin`` and ``--projtmax`` are
+ relative to the time point of the event rather than the whole raw
+ data file.
+
+**\---projtmin <time/s>**
+
+ Specify the beginning time for the calculation of the covariance matrix
+ which serves as the basis for the new SSP operator. This option
+ is required with ``--projevent`` and defaults to the beginning
+ of the raw data file otherwise. This option is effective only if ``--makeproj`` or ``--saveprojtag`` options
+ are present.
+
+**\---projtmax <time/s>**
+
+ Specify the ending time for the calculation of the covariance matrix which
+ serves as the basis for the new SSP operator. This option is required
+ with ``--projevent`` and defaults to the end of the raw data
+ file otherwise. This option is effective only if ``--makeproj`` or ``--saveprojtag`` options
+ are present.
+
+**\---projngrad <number>**
+
+ Number of SSP components to include for planar gradiometers (default
+ = 5). This value is system dependent. For example, in a well-shielded
+ quiet environment, no planar gradiometer projections are usually
+ needed.
+
+**\---projnmag <number>**
+
+ Number of SSP components to include for magnetometers / axial gradiometers
+ (default = 8). This value is system dependent. For example, in a
+ well-shielded quiet environment, 3 - 4 components are need
+ while in a noisy environment with light shielding even more than
+ 8 components may be necessary.
+
+**\---projgradrej <value/ fT/cm>**
+
+ Rejection limit for planar gradiometers in the estimation of the covariance
+ matrix frfixom which the new SSP operator is derived. The default
+ value is 2000 fT/cm. Again, this value is system dependent.
+
+**\---projmagrej <value/ fT>**
+
+ Rejection limit for planar gradiometers in the estimation of the covariance
+ matrix from which the new SSP operator is derived. The default value
+ is 3000 fT. Again, this value is system dependent.
+
+**\---saveprojtag <tag>**
+
+ This option defines the names of files to hold the SSP operator.
+ If this option is present the ``--makeproj`` option is
+ implied. The SSP operator file name is formed by removing the trailing ``.fif`` or ``_raw.fif`` from
+ the raw data file name by appending <tag> .fif
+ to this stem. Recommended value for <tag> is ``-proj`` .
+
+**\---saveprojaug**
+
+ Specify this option if you want to use the projection operator file output
+ in the Elekta-Neuromag Signal processor (graph) software.
+
+**\---eventsout <name>**
+
+ List the digital trigger channel events to the specified file. By default,
+ only transitions from zero to a non-zero value are listed. If multiple
+ raw data files are specified, an equal number of ``--eventsout`` options
+ should be present. If the file name ends with .fif, the output will
+ be in fif format, otherwise a text event file will be output.
+
+**\---allevents**
+
+ List all transitions to file specified with the ``--eventsout`` option.
+
+**\---events <name>**
+
+ Specifies the name of a fif or text format event file (see :ref:`CACBCEGC`) to be associated with a raw data file to be
+ processed. If multiple raw data files are specified, the number
+ of ``--events`` options can be smaller or equal to the
+ number of raw data files. If it is equal, the event filenames will
+ be associated with the raw data files in the order given. If it
+ is smaller, the remaining raw data files for which an event file
+ is not specified will *not* have an event file associated
+ with them. The event file format is recognized from the file name:
+ if it ends with ``.fif`` , the file is assumed to be in
+ fif format, otherwise a text file is expected.
+
+**\---ave <name>**
+
+ Specifies the name of an off-line averaging description file. For details
+ of the format of this file, please consult :ref:`CACBBDGC`.
+ If multiple raw data files are specified, the number of ``--ave`` options
+ can be smaller or equal to the number of raw data files. If it is
+ equal, the averaging description file names will be associated with
+ the raw data files in the order given. If it is smaller, the last
+ description file will be used for the remaining raw data files.
+
+**\---saveavetag <tag>**
+
+ If this option is present and averaging is evoked with the ``--ave`` option,
+ the outfile and logfile options in the averaging description file
+ are ignored. Instead, trailing ``.fif`` or ``_raw.fif`` is
+ removed from the raw data file name and <tag> ``.fif`` or <tag> ``.log`` is appended
+ to create the output and log file names, respectively.
+
+**\---gave <name>**
+
+ If multiple raw data files are specified as input and averaging
+ is requested, the grand average over all data files will be saved
+ to <name> .
+
+**\---cov <name>**
+
+ Specify the name of a description file for covariance matrix estimation. For
+ details of the format of this file, please see :ref:`CACEBACG`.
+ If multiple raw data files are specified, the number of ``--cov`` options can
+ be smaller or equal to the number of raw data files. If it is equal, the
+ averaging description file names will be associated with the raw data
+ files in the order given. If it is smaller, the last description
+ file will be used for the remaining raw data files.
+
+**\---savecovtag <tag>**
+
+ If this option is present and covariance matrix estimation is evoked with
+ the ``--cov`` option, the outfile and logfile options in
+ the covariance estimation description file are ignored. Instead,
+ trailing ``.fif`` or ``_raw.fif`` is removed from
+ the raw data file name and <tag> .fif or <tag> .log
+ is appended to create the output and log file names, respectively.
+ For compatibility with other MNE software scripts, ``--savecovtag -cov`` is recommended.
+
+**\---savehere**
+
+ If the ``--saveavetag`` and ``--savecovtag`` options
+ are used to generate the file output file names, the resulting files
+ will go to the same directory as raw data by default. With this
+ option the output files will be generated in the current working
+ directory instead.
+
+**\---gcov <name>**
+
+ If multiple raw data files are specified as input and covariance matrix estimation
+ is requested, the grand average over all data files will be saved
+ to <name> . The details of
+ the covariance matrix estimation are given in :ref:`CACHAAEG`.
+
+**\---save <name>**
+
+ Save a filtered and optionally down-sampled version of the data
+ file to <name> . If multiple
+ raw data files are specified, an equal number of ``--save`` options
+ should be present. If <filename> ends
+ with ``.fif`` or ``_raw.fif`` , these endings are
+ deleted. After these modifications, ``_raw.fif`` is inserted
+ after the remaining part of the file name. If the file is split
+ into multiple parts (see ``--split`` option below), the
+ additional parts will be called <name> ``-`` <number> ``_raw.fif``
+
+**\---split <size/MB>**
+
+ Specifies the maximum size of the raw data files saved with the ``--save`` option.
+ By default, the output is split into files which are just below
+ 2 GB so that the fif file maximum size is not exceed.
+
+**\---anon**
+
+ Do not include any subject information in the output files created with
+ the ``--save`` option.
+
+**\---decim <number>**
+
+ The data are decimated by this factor before saving to the file
+ specified with the ``--save`` option. For decimation to
+ succeed, the data must be lowpass filtered to less than third of
+ the sampling frequency effective after decimation.
+
+The user interface
+##################
+
+.. figure:: picture.png
+ :alt: none
+
+ The user interface of mne_browse_raw
+
+The mne_browse_raw user
+interface contains the following areas:
+
+- The menu bar.
+
+- The data display area.
+
+- Viewing and averaging tools.
+
+- Message line.
+
+The viewing and averaging tools allow quick browsing of the
+raw data with triggers, adding new triggers, and averaging on a
+single trigger.
+
+The File menu
+#############
+
+.. _CACDCHAJ:
+
+Open
+====
+
+Selecting Open from file
+menu pops up the dialog shown in :ref:`CACBHGFE`.
+
+The Raw files and Maxfilter output buttons change the file name filter to include
+names which end with ``_raw.fif`` or ``sss.fif`` ,
+respectively, to facilitate selection of original raw files or those
+processed with the Neuromag Maxfilter (TM) software
+
+The options under Software gradient compensation allow
+selection of the compensation grade for the data. These selections
+apply to the CTF data only. The standard choices are No compensation and Third-order gradient. If
+other than No compensation is
+attempted for non-CTF data, an error will be issued. The compensation
+selection affects the averages and noise-covariance matrices subsequently
+computed. The desired compensation takes effect independent of the
+compensation state of the data in the file, *i.e.*,
+already compensated data can be uncompensated and vice versa. For more
+information on software gradient compensation please consult Section 9.2.4.
+
+The Keep the initial skip button
+controls how the initial segment of data not stored in the raw data
+file is handled. During the MEG acquisition data are collected continuously
+but saving to the raw data file is controlled by the Record raw button. Initial skip refers to the segment
+of data between the start of the recording and the first activation
+of Record raw . If Keep initial skip is set, this empty segment is taken into
+account in timing, otherwise time zero is set to the beginning of
+the data stored to disk.
+
+When a raw data file is opened, the digital trigger channel
+is scanned for events. For large files this may take a while.
+
+.. note:: After scanning the trigger channel for events, mne_browse_raw and mne_process_raw produce a fif file containing the event information. This file will be called <raw data file name without fif extension> ``-eve.fif`` . If the same raw data file is opened again, this file will be consulted for event information thus making it unnecessary to scan through the file for trigger line events.
+
+.. note:: You can produce the fif event file by running mne_process_raw as follows: ``mne_process_raw --raw`` <raw data file> . The fif format event files can be read and written with the mne_read_events and mne_write_events functions in the MNE Matlab toolbox, see Chapter 10.
+
+.. _CACBHGFE:
+
+.. figure:: picture.png
+ :alt: none
+
+ The Open dialog.
+
+.. _BABJEJDG:
+
+Open evoked
+===========
+
+This menu item brings up a standard file selection dialog
+to load evoked-response data from files. All data sets from a file
+are loaded automatically and display in the average view window,
+see :ref:`CACDADBA`. The data loaded are affected by the
+scale settings, see, :ref:`CACBEHCD`, the filter, see :ref:`CACCDBBG`, and the options selected in the Manage averages dialog, see :ref:`CACJFADF`.
+
+.. _CACBDDIE:
+
+Save
+====
+
+It is possible to save filtered and projected data into a
+new raw data file. When you invoke the save option from the file
+menu, you will be prompted for the output file name and a down-sampling
+factor. The sampling frequency after down-sampling must be at least
+three times the lowpass filter corner frequency. The output will
+be split into files which are just below 2 GB so that the fif file
+maximum size is not exceed.
+
+If <filename> ends
+with ``.fif`` or ``_raw.fif`` , these endings are
+deleted. After these modifications, ``_raw.fif`` is inserted
+after the remaining part of the file name. If the file is split
+into multiple parts, the additional parts will be called <name> ``-`` <number> ``_raw.fif`` .
+For downsampling and saving options in mne_process_raw ,
+see :ref:`CACFAAAJ`.
+
+Change working directory
+========================
+
+Brings up a file selection dialog which allows changing of
+the working directory.
+
+.. _CACDFJDA:
+
+Read projection
+===============
+
+Selecting Read projection... from
+the File menu, pops up a dialog
+to enter a name of a file containing a signal-space projection operator
+to be applied to the data. There is an option to keep existing projection
+items.
+
+.. note:: Whenever EEG channels are present in the data, a projection item corresponding to the average EEG reference is automatically added.
+
+Save projection
+===============
+
+The Save projection... item
+in the File menu pops up a dialog
+to save the present projection operator into a file. Normally, the
+EEG average reference projection is not included. If you want to
+include it, mark the Include EEG average reference option.
+If your MEG projection includes items for both magnetometers and
+gradiometers and you want to use the projection operator file output
+from here in the Neuromag Signal processor (graph) software,
+mark the Enforce compatibility with graph option.
+
+Apply bad channels
+==================
+
+Applies the current selection of bad channels to the currently
+open raw file.
+
+Load events (text)
+==================
+
+Reads a text format event file. For more information on events,
+see :ref:`BABDFAHA`.
+
+Load events (fif)
+=================
+
+Reads a fif format event file. For more information on events,
+see :ref:`BABDFAHA`.
+
+.. _CACJGIFA:
+
+Save events (text)
+==================
+
+Brings up a a dialog to save all or selected types of events
+into a text file. This file can be edited and used in the averaging
+and covariance matrix estimation as an input file to specify the
+time points of events, see :ref:`CACBCEGC`. For more information
+on events, see :ref:`BABDFAHA`.
+
+Save events (fif)
+=================
+
+Save the events in fif format. These binary event files can
+be read and written with the mne_read_events and mne_write_events functions
+in the MNE Matlab toolbox, see Chapter 10.For more information
+on events, see :ref:`BABDFAHA`.
+
+.. _CACFHAFH:
+
+Load derivations
+================
+
+This menu choice allows loading of channel derivation data
+files created with the mne_make_derivations utility,
+see Section 11.5, or using the interactive derivations
+editor in mne_browse_raw , see :ref:`CACJIEHI`, Most common use of derivations is to calculate
+differences between EEG channels, *i.e.*, bipolar
+EEG data. Since any number of channels can be included in a derivation
+with arbitrary weights, other applications are possible as well.
+Before a derivation is accepted to use, the following criteria have
+to be met:
+
+- All channels to be combined into a single
+ derivation must have identical units of measure.
+
+- All channels in a single derivation have to be of the same
+ kind, *e.g.*, MEG channels or EEG channels.
+
+- All channels specified in a derivation have to be present
+ in the currently loaded data set.
+
+Multiple derivation data files can be loaded by specifying
+the Keep previous derivations option in
+the dialog that specifies the derivation file to be loaded. After
+a derivation file has been successfully loaded, a list of available
+derivations will be shown in a message dialog.
+
+Each of the derived channels has a name specified when the
+derivation file was created. The derived channels can be included
+in channel selections, see :ref:`CACCJEJD`. At present, derived
+channels cannot be displayed in topographical data displays. Derived
+channels are not included in averages or noise covariance matrix
+estimation.
+
+.. note:: If the file ``$HOME/.mne/mne_browse_raw-deriv.fif`` exists and contains derivation data, it is loaded automatically when mne_browse_raw starts unless the ``--deriv`` option has been used to specify a nonstandard derivation file, see :ref:`CACCHAGA`.
+
+Save derivations
+================
+
+Saves the current derivations into a file.
+
+Load channel selections
+=======================
+
+This choice loads a new set of channel selections. The default
+directory for the selections is $HOME/.mne. If this directory does
+not exist, it will be created before bringing up the file selection
+dialog to load the selections.
+
+.. _CACDDCGF:
+
+Save channel selections
+=======================
+
+This choice brings up a dialog to save the current channel
+selections. This is particularly useful if the standard set of selections
+has been modified as explained in :ref:`CACCJEJD`. The default
+directory for the selections is $HOME/.mne. If this directory does
+not exist, it will be created before bringing up the file selection
+dialog to save the selections. Note that all currently existing
+selections will be saved, not just those added to the ones initially
+loaded.
+
+Quit
+====
+
+Exits the program without questions asked.
+
+The Adjust menu
+###############
+
+.. _CACCDBBG:
+
+Filter
+======
+
+Selecting Filter... from
+the Adjust menu pops up the dialog
+shown in :ref:`CACCEEGI`.
+
+.. _CACCEEGI:
+
+.. figure:: picture.png
+ :alt: none
+
+ The filter adjustment dialog.
+
+The items in the dialog have the following functions:
+
+**Highpass (Hz)**
+
+ The half-amplitude point of the highpass filter. The width of the transition
+ from zero to one can be specified with the ``--highpassw`` command-line
+ option, see :ref:`CACHCFEG`. Lowest feasible highpass value
+ is constrained by the length of the filter and sampling frequency.
+ You will be informed when you press OK or Apply if
+ the selected highpass could not be realized. The default value zero means
+ no highpass filter is applied in addition to the analog highpass
+ present in the data.
+
+**Lowpass (Hz)**
+
+ The half-amplitude point of the lowpass filter.
+
+**Lowpass transition (Hz)**
+
+ The width of the INLINE_EQUATION-shaped transition
+ from one to zero, centered at the Lowpass value.
+
+**Filter active**
+
+ Selects whether or not the filter is applied to the data.
+
+The filter is realized in the frequency domain and has a
+zero phase shift. When a filter is in effect, the value of the first
+sample in the file is subtracted from the data to correct for an
+initial dc offset. This procedure also eliminates any filter artifacts
+in the beginning of the data.
+
+.. note:: The filter affects both the raw data and evoked-response data loaded from files. However, the averages computed in mne_browse_raw and shown in the topographical display are not refiltered if the filter is changed after the average was computed.
+
+.. _CACBEHCD:
+
+Scales
+======
+
+Selecting Scales... from
+the Adjust menu pops up the dialog
+shown in :ref:`CACBJGBA`.
+
+.. _CACBJGBA:
+
+.. figure:: picture.png
+ :alt: none
+
+ The Scales dialog.
+
+The items in the dialog have the following functions:
+
+**MEG (fT/cm)**
+
+ Sets the scale for MEG planar gradiometer channels in fT/cm. All scale
+ values are defined from zero to maximum, *i.e.*,
+ the viewport where signals are plotted in have the limits ±<scale value> .
+
+**MEG axmult (cm)**
+
+ The scale for MEG magnetometers and axial gradiometers is defined
+ by multiplying the gradiometer scale by this number, yielding units
+ of fT.
+
+**EEG (INLINE_EQUATION)**
+
+ The scale for EEG channels in INLINE_EQUATION.
+
+**EOG (INLINE_EQUATION)**
+
+ The scale for EOG channels in INLINE_EQUATION.
+
+**ECG (mV)**
+
+ The scale for ECG channels in mV.
+
+**EMG (mV)**
+
+ The scale for EMG channels in mV.
+
+**MISC (V)**
+
+ The scale for MISC channels in V.
+
+**Time span (s)**
+
+ The length of raw data displayed in the main window at a time.
+
+**Show stimulus markers**
+
+ Draw vertical lines at time points where the digital trigger channel has
+ a transition from zero to a nonzero value.
+
+**Segment min. time (s)**
+
+ It is possible to show data segments in the topographical (full
+ view) layout, see below. This parameter sets the starting time point,
+ relative to the selected time, to be displayed.
+
+**Segment max. time (s)**
+
+ This parameter sets the ending time point, relative to the current time,
+ to be displayed in the topographical layout.
+
+**Show segments in full view**
+
+ Switches on the display of data segments in the topographical layout.
+
+**Show segments in sample view**
+
+ Switches on the display of data segments in a "sidebar" to
+ the right of the main display.
+
+**Show channel names**
+
+ Show the names of the channels in the topographical displays.
+
+**Text size**
+
+ Size of the channel number text as a fraction of the height of each viewport.
+
+**Show viewport frames**
+
+ Show the boundaries of the viewports in the topographical displays.
+
+**Show zeroline and zerolevel**
+
+ Show the zero level, *i.e.*, the baseline level
+ in the topographical displays. In addition, the zero time point
+ is indicated in the average views if it falls to the time range, *i.e.*,
+ if the minimum of the time scale is negative and the maximum is
+ positive.
+
+**Scale magnification for averages**
+
+ For average displays, the scales are made more sensitive by this
+ factor.
+
+**Average display baseline min (ms)**
+
+ Sets the lower time limit for the average display baseline. This
+ setting does not affect the averages stored.
+
+**Average display baseline max (ms)**
+
+ Sets the upper time limit for the average display baseline. This
+ setting does not affect the averages stored.
+
+**Use average display baseline**
+
+ Switches the application of a baseline to the displayed averages
+ on and off.
+
+**Average time range min (ms)**
+
+ Sets the minimum time for the average display. This setting is inactive
+ if Autoscale time range is on.
+
+**Average time range max (ms)**
+
+ Sets the maximum time for the average data display. This setting
+ is inactive if Autoscale time range is
+ on.
+
+**Autoscale time range**
+
+ Set the average display time range automatically to be long enough to
+ accommodate all data.
+
+Colors
+======
+
+Shows a dialog which allows changes to the default colors
+of various display items.
+
+.. _CACJIEHI:
+
+Derivations
+===========
+
+Brings up the interactive derivations editor. This editor
+can be used to add or modify derived channels, *i.e.*,
+linear combinations of signals actually recorded. Channel derivations
+can be also created and modified using the mne_make_derivations tool,
+see Section 11.5. The interactive editor contains two main
+areas:
+
+- Interactive tools for specifying a channel
+ linear combination. This tool is limited to combining up to five
+ channels in each of the derivations. Clicking Add after
+ defining the name of the new derivation, the weights of the component
+ channels and their names, adds the corresponding arithmetic expression
+ to the text area.
+
+- Text area which contains the currently defined derivations
+ as arithmetic expressions in a format identical to that used by mne_make_derivations .
+ These expressions can be manually edited before accepting the new
+ set of derivations. Initially, the text area will contain the derivations
+ already defined.
+
+The Define button interprets
+the arithmetic expressions in the text area as new derivations and
+closes the dialog. The Cancel button
+closes the dialog without any change in the derivations.
+
+Recommended workflow for defining derived EEG channels and
+associated selections interactively involves the following steps:
+
+- If desired, EEG channels can be relabeled
+ with descriptive names using the mne_rename_channels utility,
+ see Section 11.4.5. It is strongly recommended that you
+ keep a copy of the channel alias file used by mne_rename_channels .
+ If necessary, you can then easily return to the original channel
+ names by running mne_rename_channels again
+ with the ``--revert`` option.
+
+- Load the data file into mne_browse_raw and
+ use the interactive derivations editor to create the desired derived
+ channels. These are usually differences between the signals in two
+ EEG electrodes.
+
+- Save the derivations from the file menu.
+
+- If desired, move the derivations file to the standard location
+ (``$HOME/.mne/mne_browse_raw-deriv.fif`` ).
+
+- Create new channel selections employing the original and derived channels
+ using the channel selection tool described in :ref:`CACCJEJD`.
+
+- Save the new channel selections from the file menu.
+
+- If desired, change the order of the channels in the selections
+ in the selection file by editing it in a text editor and move it
+ to the standard location ``$HOME/.mne/mne_browse_raw.sel`` .
+
+.. _CACCJEJD:
+
+Selection
+=========
+
+Brings up a dialog to select channels to be shown in the
+main raw data display. This dialog also allows modification of the
+set of channel selections as described below.
+
+By default, the available selections are defined by the file ``$MNE_ROOT/share/mne/mne_browse_raw/mne_browse_raw.sel`` .
+This default channel selection file can be modified by copying the
+file into ``$HOME/.mne/mne_browse_raw.sel`` . The format
+of this text file should be self explanatory.
+
+.. _CACIHFFH:
+
+.. figure:: picture.png
+ :alt: none
+
+ The channel selection dialog.
+
+The channel selection dialog is shown in :ref:`CACIHFFH`.
+The number of items in the selection list depends on the contents
+of your selection file. If the list has the keyboard focus you can
+easily move from one selection to another with the up and down arrow
+keys.
+
+The two buttons below the channel selection buttons facilitate
+the modification of the selections:
+
+**Add...**
+
+ Brings up the selection dialog shown in :ref:`CACFECED` to
+ create new channel selections.
+
+**Omit current**
+
+ Delete the current channel selection. Deletion only affects the
+ selections in the memory of the program. To save the changes permanently
+ into a file, use Save channel selections... in
+ the File menu, see :ref:`CACDDCGF`.
+
+.. _CACFECED:
+
+.. figure:: picture.png
+ :alt: none
+
+ Dialog to create a new channel selection.
+
+The components of the selection creation dialog shown in :ref:`CACFECED` have the following functions:
+
+**List of channel names**
+
+ The channels selected from this list will be included in the new channel
+ selection. A selection can be extended with the control key. A range
+ of channels can be selected with the shift key. The list contains
+ both the original channels actually present in the file and the names
+ of the channels in currently loaded derivation data, see :ref:`CACFHAFH`.
+
+**Regexp:**
+
+ This provides another way to select channels. By entering here a regular
+ expression as defined in IEEE Standard 1003.2 (POSIX.2), all channels
+ matching it will be selected and added to the present selection.
+ An empty expression deselects all items in the channel list. Some
+ useful regular expressions are listed in :ref:`CACHCHDJ`.
+ In the present version, regular matching does not look at the derived
+ channels.
+
+**Name:**
+
+ This text field specifies the name of the new selection.
+
+**Select**
+
+ Select the channels specified by the regular expression. The same effect
+ can be achieved by entering return in the Regexp: .
+
+**Add**
+
+ Add a new channel selection which contains the channels selected from
+ the channel name list. The name of the selection is specified with
+ the Name: text field.
+
+.. _CACHCHDJ:
+
+.. table:: Examples of regular expressions for channel selections
+
+ ==================== =================================================================================================
+ Regular expression Meaning
+ ==================== =================================================================================================
+ ``MEG`` Selects all MEG channels.
+ ``EEG`` Selects all EEG channels.
+ ``MEG.*1$`` Selects all MEG channels whose names end with the number 1, *i.e.*, all magnetometer channels.
+ ``MEG.*[2,3]$`` Selects all MEG gradiometer channels.
+ ``EEG|STI 014`` Selects all EEG channels and stimulus channel STI 014.
+ ``^M`` Selects all channels whose names begin with the letter M.
+ ==================== =================================================================================================
+
+.. note:: The interactive tool for creating the channel selections does not allow you to change the order of the selected channels from that given by the list of channels. However, the ordering can be easily changed by manually editing the channel selection file in a text editor.
+
+.. _CACFGGCF:
+
+Full view layout
+================
+
+Shows a selection of available layouts for the topographical
+views (full view and average display). The system-wide layout files
+reside in ``$MNE_ROOT/share/mne/mne_analyze/lout`` . In
+addition any layout files residing in ``$HOME/.mne/lout`` are
+listed. The default layout is Vectorview-grad. If there is a layout
+file in the user's private layout directory ending with ``-default.lout`` ,
+that layout will be used as the default instead. The Default button
+returns to the default layout.
+
+The format of the layout files is:
+
+<plot area limits> <viewport definition #1>
+...<viewport definition #N>
+
+The <plot area limits> define
+the size of the plot area (INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION INLINE_EQUATION)
+which should accommodate all view ports. When the layout is used, the
+plot area will preserve its aspect ratio; if the plot window has
+a different aspect ratio, there will be empty space on the sides.
+
+The viewports define the locations of the individual channels
+in the plot. Each viewport definition consists of
+
+<number> INLINE_EQUATION INLINE_EQUATION <width> <height> < name> [:<name> ]...
+
+where number is a viewport number (not used by the MNE software), INLINE_EQUATION and INLINE_EQUATION are
+the coordinates of the lower-left corner of the viewport, <width> and <height> are
+the viewport dimensions, and <name> is
+a name of a channel. Multiple channel names can be specified by
+separating them with a colon.
+
+When a measurement channel name is matched to a layout channel
+name, all spaces are removed from the channel names and the both
+the layout channel name and the data channel name are converted
+to lower case. In addition anything including and after a hyphen
+(-) is omitted. The latter convention facilitates using CTF MEG
+system data, which has the serial number of the system appended
+to the channel name with a dash. Removal of the spaces is important
+for the Neuromag Vectorview data because newer systems do not have
+spaces in the channel names like the original Vectorview systems
+did.
+
+.. note:: The mne_make_eeg_layout utility can be employed to create a layout file matching the positioning of EEG electrodes, see Section 11.6.
+
+.. _CACDDIDH:
+
+Projection
+==========
+
+Lists the currently available signal-space projection (SSP)
+vectors and allows the activation and deactivation of items. For
+more information on SSP, see :ref:`CACCHABI`.
+
+Compensation
+============
+
+Brings up a dialog to select software gradient compensation.
+This overrides the choice made at the open time. For details, see :ref:`CACDCHAJ`, above.
+
+.. _CACBIAHD:
+
+Averaging preferences
+=====================
+
+.. _CACCFFAH:
+
+.. figure:: picture.png
+ :alt: none
+
+ Averaging preferences.
+
+Selecting Averaging preferences... from
+the Adjust menu pops up the dialog
+shown in :ref:`CACCFFAH`. These settings apply only to the
+simple averages calculated with help of tools residing just below
+the main raw data display, see :ref:`CACDFGAE`. These settings
+are also applied when a covariance matrix is computed to create
+a SSP operator as described in :ref:`CACEAHEI` and in the
+computation of a covariance matrix from raw data, see :ref:`BABJEIGJ`.
+
+The items in the dialog have the following functions:
+
+**Starting time (ms)**
+
+ Beginning time of the epoch to be averaged (relative to the trigger).
+
+**Ending time (ms)**
+
+ Ending time of the epoch to be averaged.
+
+**Ignore around stimulus (ms)**
+
+ Ignore this many milliseconds on both sides of the trigger when considering
+ the epoch. This parameter is useful for ignoring large stimulus
+ artefacts, *e.g.*, from electrical somatosensory
+ stimulation.
+
+**MEG grad rejection (fT/cm)**
+
+ Rejection criterion for MEG planar gradiometers. If the peak-to-peak
+ value of any planar gradiometer epoch exceed this value, it will
+ be omitted. A negative value turns off rejection for a particular channel
+ type.
+
+**MEG mag rejection (fT)**
+
+ Rejection criterion for MEG magnetometers and axial gradiometers.
+
+**EEG rejection ( INLINE_EQUATIONV)**
+
+ Rejection criterion for EEG channels.
+
+**EOG rejection ( INLINE_EQUATIONV)**
+
+ Rejection criterion for EOG channels.
+
+**ECG rejection (mV)**
+
+ Rejection criterion for ECG channels.
+
+**MEG grad no signal (fT/cm)**
+
+ Signal detection criterion for MEG planar gradiometers. The peak-to-peak
+ value of all planar gradiometer signals must exceed this value,
+ for the epoch to be included. This criterion allows rejection of data
+ with saturated or otherwise dysfunctional channels.
+
+**MEG mag no signal (fT)**
+
+ Signal detection criterion for MEG magnetometers and axial gradiometers.
+
+**EEG no signal ( INLINE_EQUATIONV)**
+
+ Signal detection criterion for EEG channels.
+
+**EOG no signal ( INLINE_EQUATIONV)**
+
+ Signal detection criterion for EOG channels.
+
+**ECG no signal (mV)**
+
+ Signal detection criterion for ECG channels.
+
+**Fix trigger skew**
+
+ This option has the same effect as the FixSkew parameter
+ in averaging description files, see :ref:`BABIHFBI`.
+
+**Trace color**
+
+ The color assigned for the averaged traces in the display can be adjusted
+ by pressing this button.
+
+The Process menu
+################
+
+Averaging
+=========
+
+The Average... menu item
+pops up a file selection dialog to access a description file for
+batch-mode averaging. The structure of these files is described
+in :ref:`CACBBDGC`. All parameters for the averaging are
+taken from the description file, *i.e.*, the
+parameters set in the averaging preferences dialog (:ref:`CACBIAHD`) do not effect the result.
+
+Estimation of a covariance matrix
+=================================
+
+The Compute covariance... menu
+item pops up a file selection dialog to access a description file
+which specifies the options for the estimation of a covariance matrix.
+The structure of these files is described in :ref:`CACEBACG`.
+
+.. _BABJEIGJ:
+
+Estimation of a covariance matrix from raw data
+===============================================
+
+The Compute raw data covariance... menu
+item pops up a dialog which specifies a time range for raw data
+covariance matrix estimation and the file to hold the result. If
+a covariance matrix is computed in this way, the rejection parameters
+specified in averaging preferences are in effect. For description
+of the rejection parameters, see :ref:`CACBIAHD`. The time
+range can be also selected interactively from the main raw data
+display by doing a range selection with shift left button drag.
+
+.. _CACEAHEI:
+
+Creating a new SSP operator
+===========================
+
+The Create a new SSP operator... menu
+choice computes a new SSP operator as discussed in :ref:`BABFFCHF`.
+
+.. _BABHAGHF:
+
+.. figure:: picture.png
+ :alt: none
+
+ Time range specification for SSP operator calculation
+
+When Create a new SSP operator... selected,
+a window shown in :ref:`BABHAGHF` is popped up. It allows
+the specification of a time range to be employed in the calculation
+of a raw data covariance matrix. The time range can be also selected
+interactively from the main raw data display by doing a range selection
+with shift left button drag. Normally, you should use empty room
+data for this computation. For the estimation of the covariance
+matrix any existing projection will be temporarily switched off. Remember
+to inspect your data for bad channels and select an appropriate filter
+setting before creating a new SSP operator. The artifact rejection parameters
+specified averaging preferences will be applied in the covariance
+matrix calculation, see :ref:`CACBIAHD`.
+
+Instead of using continuous raw data, it is also possible
+to employ short epochs around triggers (events) in the calculation
+of the new SSP operator by specifying a positive event number in
+the time specification dialog. This option is very useful, *e.g.*,
+to remove MCG/ECG artifacts from the data to facilitate detection
+of epileptic spikes:
+
+- Select left or right temporal channels
+ to the display.
+
+- Mark several peaks of the MCG signal in the data: click on
+ the first one and control click on the subsequent ones to extend
+ the selection.
+
+- Select an event number next to the Picked to button in the tool bar, see :ref:`CACDFGAE`,
+ and click Picked to . As a result
+ the lines marking the events will change color (by default from
+ green to blue) indicating transition to user-created events.
+
+- Specify an epoch time range to be employed and the event number selected
+ in the previous step for the SSP operator calculation.
+
+Once the parameters are set, click Compute to
+calculate a covariance matrix according to you your specifications.
+Once the covariance matrix is ready, the parts corresponding to
+magnetometer or axial gradiometer, planar gradiometer, and EEG channels
+are separated and the corresponding eigenvectors and eigenvalues
+are computed. Once complete, a projection selector with eight magnetometer
+eigenvectors, five planar gradiometer eigenvectors, three EEG eigenvectors,
+as well as the existing projection items is displayed.
+
+Using the projection selector, you can experiment which vectors
+have a significant effect on the noise level of the data. You should
+strive for using a minimal number of vectors. When the selection
+is complete, you can click Accept to
+introduce this selection of vectors as the new projection operator. Discard abandons
+the set of calculated vectors. Whenever EEG channels are present
+in the data, a projection item corresponding to the average EEG
+reference is automatically added when a new projection operator
+is introduced. More information on the SSP method can be found in :ref:`CACCHABI`.
+
+.. note:: The new projection data created in mne_browse_raw is not automatically copied to the data file. You need to create a standalone projection file from File/Save projection... to save the new projection data and load it manually after the data file has been loaded if you want to include in any subsequent analysis.
+
+.. note:: The command-line options for mne_process_raw allow calculation of the SSP operator from continuous data in the batch mode, see :ref:`CACFAAAJ`.
+
+.. _BABDJGGJ:
+
+The Windows menu
+################
+
+The Windows menu contains
+the following items:
+
+**Show full view...**
+
+ Brings up the topographical display of epochs extracted from the raw
+ data, see :ref:`CACDADBA`.
+
+**Show averages...**
+
+ Brings up the topographical display showing averaged data. These data
+ may include data averaged in the current mne_browse_raw session
+ or those loaded from files, see :ref:`BABJEJDG`.
+
+**Show event list...**
+
+ Brings up a window containing a list of the currently defined events. Clicking
+ on an event in the list, the event is selected, a green cursor appears
+ at the event, and the event is brought to the middle of the raw
+ data display. The event list displayed can be also restricted to user-defined
+ events (annotations) and user-defined events can be deleted. For
+ further information, see :ref:`BABDFAHA`.
+
+**Show annotator...**
+
+ Brings up a window which allows adding new events to the data with
+ annotations or comments. For details, see :ref:`BABDFAHA`.
+
+**Manage averages...**
+
+ Brings up a dialog to control the averaged data sets, see :ref:`CACJFADF`.
+
+**Start mne_analyze...**
+
+ Start interaction between mne_browse_raw and mne_analyze .
+ For details, see :ref:`CACGHEGC`.
+
+**Show head position**
+
+ Starts mne_analyze in the head position visualization mode and shows
+ the relative position of the MEG sensor array and the head using
+ the data in the presently open raw data file. For more details on
+ the head position visualization mode, see Section 7.21.
+
+**Quit mne_analyze...**
+
+ Quits the mne_analyze program
+ started with Start mne_analyze...
+
+The Help menu
+#############
+
+The contents of the Help menu
+is shown in :ref:`CACGFEAF`:
+
+.. _CACGFEAF:
+
+.. figure:: picture.png
+ :alt: none
+
+ The Help menu.
+
+**On version...**
+
+ Displays the version and compilation date of the program.
+
+**On license...**
+
+ Displays the license information.
+
+**About current data...**
+
+ Displays essential information about the currently loaded data set.
+
+**Why the beep?**
+
+ In some simple error situations, mne_browse_raw does
+ not pop up an error dialog but refuses the action and rings the
+ bell. The reason for this can be displayed through this help menu
+ item.
+
+The raw data display
+####################
+
+The main data displays shows a section of the raw data in
+a strip-chart recorder format. The names of the channels displayed
+are shown on the left. The selection of channels is controlled from
+the selection dialog, see :ref:`CACCJEJD`. The length of
+the data section displayed is controlled from the scales dialog
+(:ref:`CACBEHCD`) and the filtering from the filter dialog (:ref:`CACCDBBG`). A signal-space projection can be applied
+to the data by loading a projection operator (:ref:`CACDFJDA`).
+The selection of the projection operator items is controlled from
+the projection dialog described in :ref:`CACDDIDH`.
+
+The control and browsing functions of the main data display
+are:
+
+**Selection of bad channels**
+
+ If you click on a channel name the corresponding channel is marked bad
+ or reinstated as an acceptable one. A channel marked bad is not considered
+ in the artefact rejection procedures in averaging and it is omitted
+ from the signal-space projection operations.
+
+**Browsing**
+
+ Browsing through the data. The section of data displayed can be selected
+ from the scroll bar at the bottom of the display. Additional browsing
+ functionality will be discussed n In addition, if the strip-chart
+ display has the keyboard focus, you can scroll back and forth with
+ the page up and page down keys.
+
+**Selection of time points**
+
+ When you click on the data with the left button, a vertical marker appears.
+ If Show segments in full view and/or Show segments in sample view is active in the scales
+ dialog (see :ref:`CACBEHCD`), a display of an epoch of data
+ specified in the scales dialog will appear. For more information
+ on full view, see :ref:`CACDADBA`. Multiple time points can
+ be selected by holding the control key down when clicking. If multiple
+ time points are selected several samples will be shown in the sample
+ and/or full view, aligned at the picked time point. The tool bar
+ offers functions to operate on the selected time points, see :ref:`CACDFGAE`.
+
+**Range selection**
+
+ Range selection. If you drag on the signals with the left mouse
+ button and the shift key down, a range of times will be selected
+ and displayed in the sample and/or full view. Note: All previous
+ selections are cleared by this operation.
+
+**Saving a copy of the display**
+
+ The right mouse button invokes a popup menu which allows saving of
+ the display in various formats. Best quality is achieved with the Illustrator
+ format. This format has the benefit that it is object oriented and
+ can be edited in Adobe Illustrator.
+
+**Drag and drop**
+
+ Graphics can be moved to one of the Elekta-Neuromag report composer
+ (cliplab ) view areas with the
+ middle mouse button.
+
+.. note:: When selecting bad channels, switch the signal-space projection off from the projection dialog. Otherwise bad channels may not be easily recognizable.
+
+.. note:: The cliplab drag-and-drop functionality requires that you have the proprietary Elekta-Neuromag analysis software installed. mne_browse_raw is compatible with cliplab versions 1.2.13 and later.
+
+.. _BABIDADB:
+
+Browsing data
+=============
+
+If the strip-chart display has
+the input focus (click on it, if you are unsure) the keyboard and
+mouse can be used to browse the data as follows:
+
+**Up and down arrow keys**
+
+ Activate the previous or next selection in the selection list.
+
+**Left and right arrow keys**
+
+ If a single time point is selected (green line), move the time point forward
+ and backward by INLINE_EQUATION. If the shift
+ key is down, the time point is moved by INLINE_EQUATION.
+ If the control key is down (with or without shift), the time point
+ is moved by INLINE_EQUATION. If mne_browse_raw is
+ controlling mne_analyze (see :ref:`CACGHEGC`), the mne_analyze displays
+ will be updated accordingly. If the picked time point falls outside
+ the currently displayed section of data, the display will be automatically
+ scrolled backwards or forwards as needed.
+
+**Rotate the mouse wheel or rotate the trackball up/down**
+
+ Activate the previous or next selection in the selection list.
+
+**Rotate the trackball left/right or rotate the wheel with shift down**
+
+ Scroll backward or forward in the data by one screen. With Alt key (Command or Apple key
+ in the Mac keyboard), the amount of scrolling will be INLINE_EQUATION instead
+ of the length of one screen. If shift key is held down with the
+ trackball, both left/right and up/down movements scroll the data
+ in time.
+
+.. note:: The trackball and mouse wheel functionality is dependent on your X server settings. On Mac OSX these settings are normally correct by default but on a LINUX system some adjustments to the X server settings maybe necessary. Consult your system administrator or Google for details.
+
+.. _BABDFAHA:
+
+Events and annotations
+######################
+
+.. _BABJGEDF:
+
+Overview
+========
+
+In mne_browse_raw and mne_process_raw *events* mark
+interesting time points in the data. When a raw data file is opened,
+a standard event file is consulted for the list of events. If this
+file is not present, the digital trigger channel, defined by the --digtrig option
+or the ``MNE_TRIGGER_CH_NAME`` environment variable is
+scanned for events. For more information, see Sections :ref:`BABBGJEA` and :ref:`CACDCHAJ`.
+
+In addition to the events detected on the trigger channel,
+it is possible to associate user-defined events to the data, either
+by marking data points interactively as described in :ref:`BABCIGGH` or by loading event data from files, see :ref:`BABDGBHI`. Especially if there is a comment associated
+with a user-defined event, we will sometimes call it an *annotation*.
+
+If a data files has annotations (user-defined events) associated
+with it in mne_browse_raw , information
+about them is automatically saved to an annotation file when a data file is closed, *i.e.*,
+when you quit mne_browse_raw or
+load a new data file. This annotation file is called <raw data file name without fif extension> ``-annot.fif`` and
+will be stored in the same directory as the raw data file. Therefore,
+write permission to this directory is required to save the annotation
+file.
+
+Both the events defined by the trigger channel and the user-defined
+events have three properties:
+
+- The *time* when the
+ event occurred.
+
+- The *value* on the trigger channel just
+ before the change and now. For user-defined events the value before
+ is always zero and the current value is user defined and does not
+ necessarily reflect a change on the trigger channel. The trigger
+ channel events may also indicate changes between two non-zero values
+ and from a non-zero to zero. The event list described in :ref:`BABFDICC` shows only transitions from zero to a non-zero
+ value. Similarly, the Jump to item
+ in the tool bar, described in :ref:`CACDFGAE`, only detects
+ transitions from zero to a nonzero value.
+
+- An optional *comment* text, which is especially
+ helpful in associating user-defined events with real-world activity, *e.g.*,
+ the subject closing or opening his/her eyes or an epileptic patient
+ showing indications of a seizure.
+
+.. _BABFDICC:
+
+The event list
+==============
+
+The Windows/Show event list... menu
+choice shows a window containing a list of currently defined events.
+The list can be restricted to user-defined events by checking User-defined events only . When an event is selected from the
+list, the main display jumps to the corresponding time. If a user-defined
+event is selected, it can be deleted with the Delete a user-defined event button.
+
+.. _BABDGBHI:
+
+Loading and saving event files
+==============================
+
+Using the Load/Save events choices in the file menu, events
+can be saved in text and fif formats, see :ref:`CACBCEGC`,
+below. The loading dialogs have the following options:
+
+**Match comment with**
+
+ Only those events which will contain comments and in which the comment
+ matches the entered text are loaded. This filtering option is useful, *e.g.*,
+ in loading averaging or covariance matrix computation log files,
+ see Sections :ref:`BABIHFBI` and :ref:`BABCGEJE`.
+ If the word *omit* is entered as the filter,
+ only events corresponding to discarded epochs are loaded and the
+ reason for rejection can be investigated in detail.
+
+**Add as user events**
+
+ Add the events as if they were user-defined events. As a result,
+ the annotation file saved next time mne_browse_raw closes
+ this raw file will contain these events.
+
+**Keep existing events**
+
+ By default, the events loaded will replace the currently defined
+ ones. With this option checked, the loaded event will be merged
+ with the currently existing ones.
+
+The event saving dialogs have the
+following options controlling the data saved:
+
+**Save events read from the data file**
+
+ Save only those event which are not designated as user defined. These
+ are typically the events corresponding to changes in the digital
+ trigger channel. Another possible source for these events is an event
+ file manually loaded *without* the Add as user events option.
+
+**Save events created here**
+
+ Save the user-defined events.
+
+**Save all trigger line transitions**
+
+ By default only those events which are associate with a transition from
+ zero to non-zero value are saved. These include the user-defined
+ events and leading edges of pulses on the trigger line. When this
+ option is present, all events included with the two above options are
+ saved, regardless the type of transition indicated (zero to non-zero,
+ non-zero to another non-zero value, and non-zero value to zero).
+
+.. note:: If you have a text format event file whose content you want to include as user-defined events and create the automatic annotation file described in :ref:`BABJGEDF`, proceed as follows:
+
+- Load the event file with the option Add as user events set.
+
+- Open another data file or quit mne_browse_raw .
+
+- Optionally remove unnecessary events using the event list
+ dialog.
+
+The directory in which the raw data file resides now contains
+an annotation file which will be automatically loaded each time
+the data file is opened. A text format event file suitable for this
+purpose can be created manually, extracted from an EDF+ file using
+the ``--tal`` option in mne_edf2fiff discussed
+in Section 9.2.8, or produced by custom software used during
+data acquisition.
+
+.. _BABCIGGH:
+
+Defining annotated events
+=========================
+
+The Windows/Show annotator... shows
+a window to add annotated user-defined events. In this window, the
+buttons in first column mark one or more selected time points with
+the event number shown in the second column with an associated comment
+specified in the third column. Marking also occurs when return is
+pressed on any of the second and third column text fields.
+
+When the dialog is brought up for the first time, the file
+$HOME/.mne/mne_browse_raw.annot is consulted for the definitions
+of the second and third column values, *i.e.*,
+event numbers and comments. You can save the current definitions
+with the Save defs button and
+reload the annotation definition file with Load defs . The annotation definition file may contain comment
+lines starting with '%' or '#' and
+data lines which contain an event number and an optional comment,
+separated from the event number by a colon.
+
+.. note:: If you want to add a user-defined event without an a comment, you can use the Picked to item in the tool bar, described in :ref:`CACDFGAE`.
+
+.. _CACBCEGC:
+
+Event files
+===========
+
+A text format event file contains information about transitions
+on the digital trigger line in a raw data file. Any lines beginning
+with the pound sign (``#`` ) are considered as comments.
+The format of the event file data is:
+
+<sample> <time> <from> <to> <text>
+
+where
+
+**<sample>**
+
+ is
+ the sample number. This sample number takes into account the initial
+ empty space in a raw data file as indicated by the FIFF_FIRST_SAMPLE
+ and/or FIFF_DATA_SKIP tags in the beginning of raw data. Therefore,
+ the event file contents are independent of the Keep initial skip setting in the open dialog.
+
+**<time>**
+
+ is
+ the time from the beginning of the file to this sample in seconds.
+
+**<from>**
+
+ is
+ the value of the digital trigger channel at <sample> -1.
+
+**<to>**
+
+ is
+ the value of the digital trigger channel at <sample> .
+
+**<text>**
+
+ is
+ an optional annotation associated with the event. This comment will
+ be displayed in the event list and on the message line when you
+ move to an event.
+
+When an event file is read back, the <sample> value
+will be primarily used to specify the time. If you want the <time> to
+be converted to the sample number instead, specify a negative value
+for <sample> .
+
+Each event file starts with a "pseudo event" where
+both <from> and <to> fields
+are equal to zero.
+
+.. warning:: In previous versions of the MNE software, the event files did not contain the initial empty pseudo event. In addition the sample numbers did not take into account the initial empty space in the raw data files. The present version of MNE software is still backwards compatible with the old version of the event files and interprets the sample numbers appropriately. However, the recognition of the old and new event file formats depends on the initial pseudo [...]
+
+.. note:: If you have created Matlab, Excel or other scripts to process the event files, they may need revision to include the initial pseudo event in order for mne_browse_raw and mne_process_raw to recognize the edited event files correctly.
+
+.. note:: Events can be also stored in fif format. This format can be read and written with the Matlab toolbox functions mne_read_events and mne_write_events .
+
+.. _CACDFGAE:
+
+The tool bar
+############
+
+.. _CACCFEGH:
+
+.. figure:: picture.png
+ :alt: none
+
+ The tool bar controls.
+
+The tool bar controls are shown in :ref:`CACCFEGH`.
+They perform the following functions:
+
+**start/s**
+
+ Allows specification of the starting time of the display as a numeric value.
+ Note that this value will be rounded to the time of the nearest sample
+ when you press return. If you click on this text field, you can also
+ change the time with the up and down cursor keys (1/10 of the window
+ size), and the page up and down (or control up and down cursor)
+ keys (one window size).
+
+**Remove dc**
+
+ Remove the dc offset from the signals for display. This does not affect
+ the data used for averaging and noise-covariance matrix estimation.
+
+**Keep dc**
+
+ Return to the original true dc levels.
+
+**Jump to**
+
+ Enter a value of a trigger to be searched for. The arrow buttons
+ jump to the next event of this kind. A selection is also automatically
+ created and displayed as requested in the scales dialog, see :ref:`CACBEHCD`. If the '+' button is active,
+ previous selections are kept, otherwise they are cleared.
+
+**Picked to**
+
+ Make user events with this event number at all picked time points.
+ It is also possible to add annotated user events with help of the
+ annotation dialog. For further information, see :ref:`BABDFAHA`.
+
+**Forget**
+
+ Forget desired user events.
+
+**Average**
+
+ Compute an average to this event.
+
+The tool bar status line shows the starting time and the
+length of the window in seconds as well as the cursor time point.
+The dates and times in parenthesis show the corresponding wall-clock
+times in the time zone where mne_browse_raw is
+run.
+
+.. note:: The wall-clock times shown are based on the information in the fif file and may be offset from the true acquisition time by about 1 second. This offset is constant throughout the file. The times reflect the time zone setting of the computer used to analyze the data rather than the one use to acquire them.
+
+.. _CACDADBA:
+
+Topographical data displays
+###########################
+
+Segments of data can shown in a topographical layout in the Full view window, which can be requested from the Scale dialog
+or from the Windows menu. Another
+similar display is available to show the averaged data. The topographical
+layout to use is selected from Adjust/Full view layout... ,
+which brings up a window with a list of available layouts. The default
+layouts reside in ``$MNE_ROOT/share/mne/mne_analyze/lout`` .
+In addition any layout files residing in ``$HOME/.mne/lout`` are listed.
+The format of the layout files is the same as for the Neuromag programs xplotter and xfit .
+A custom EEG layout can be easily created with the mne_make_eeg_layout utility,
+see Section 11.6.
+
+Several actions can be performed with the mouse in the topographical data
+display:
+
+**Left button**
+
+ Shows the time and the channel name at the cursor at the bottom
+ of the window.
+
+**Left button drag with shift key**
+
+ Enlarge the view to contain only channels in the selected area.
+
+**Right button**
+
+ Brings up a popup menu which gives a choice of graphics output formats
+ for the current topographical display. Best quality is achieved
+ with the Illustrator format. This format has the benefit that it
+ is object oriented and can be edited in Adobe Illustrator.
+
+**Middle button**
+
+ Drag and drop graphics to one of the cliplab view
+ areas.
+
+.. note:: The cliplab drag-and-drop functionality requires that you have the proprietary Elekta-Neuromag analysis software installed. mne_browse_raw is compatible with cliplab versions 1.2.13 and later.
+
+.. note:: The graphics output files will contain a text line stating of the time and vertical scales if the zero level/time and/or viewport frames have been switched on in the scales dialog, see :ref:`CACBEHCD`.
+
+.. _CACBBDGC:
+
+Description files for off-line averaging
+########################################
+
+For averaging tasks more complex than those involving only
+one trigger, the averaging parameters are specified with help of
+a text file. This section describes the format of this file. A sample
+averaging file can be found in ``$MNE_ROOT/share/mne/mne_browse_raw/templates`` .
+
+Overall format
+==============
+
+Any line beginning with the pound sign (#) in this description
+file is a comment. Each parameter in the description file is defined
+by a keyword usually followed by a value. Text values consisting
+of multiple words, separated by spaces, must be included in quotation
+marks. The case of the keywords in the file does not matter. The
+ending ``.ave`` is suggested for the average description
+files.
+
+The general format of the description file is:
+
+``average {``
+<common parameters>
+``category {``
+<category definition parameters>
+``}``
+
+....``}``
+
+The file may contain arbitrarily many categories. The word ``category`` interchangeable
+with ``condition`` .
+
+.. warning:: Due to a bug that existed in some versions of the Neuromag acquisition software, the trigger line 8 is incorrectly decoded on trigger channel STI 014. This can be fixed by running mne_fix_stim14 on the raw data file before using mne_browse_raw or mne_process_raw . The bug has been fixed on Nov. 10, 2005.
+
+.. _BABIHFBI:
+
+Common parameters
+=================
+
+The average definition starts with the common parameters.
+They include:
+
+**outfile <name>**
+
+ The name of the file where the averages are to be stored. In interactive
+ mode, this can be omitted. The resulting average structure can be
+ viewed and stored from the Manage averages window.
+
+**eventfile <name>**
+
+ Optional file to contain event specifications. If this file is present, the
+ trigger events in the raw data file are ignored and this file is
+ consulted instead. The event file format is recognized from the
+ file name: if it ends with ``.fif`` , the file is assumed
+ to be in fif format, otherwise a text file is expected. The text event
+ file format is described in :ref:`CACBCEGC`.
+
+**logfile <name>**
+
+ This optional file will contain detailed information about the averaging
+ process. In the interactive mode, the log information can be viewed
+ from the Manage averages window.
+
+**gradReject <value / T/m>**
+
+ Rejection limit for MEG gradiometer channels. If the peak-to-peak amplitude
+ within the extracted epoch exceeds this value on any of the gradiometer
+ channels, the epoch will be omitted from the average.
+
+**magReject <value / T>**
+
+ Rejection limit for MEG magnetometer and axial gradiometer channels.
+ If the peak-to-peak amplitude within the extracted epoch exceeds
+ this value on any of the magnetometer or axial gradiometer channels,
+ the epoch will be omitted from the average.
+
+**eegReject <value / V>**
+
+ Rejection limit for EEG channels. If the peak-to-peak amplitude within
+ the extracted epoch exceeds this value on any of the EEG channels,
+ the epoch will be omitted from the average.
+
+**eogReject <value / V>**
+
+ Rejection limit for EOG channels. If the peak-to-peak amplitude within
+ the extracted epoch exceeds this value on any of the EOG channels,
+ the epoch will be omitted from the average.
+
+**ecgReject <value / V>**
+
+ Rejection limit for ECG channels. If the peak-to-peak amplitude within
+ the extracted epoch exceeds this value on any of the ECG channels,
+ the epoch will be omitted from the average.
+
+**gradFlat <value / T/m>**
+
+ Signal detection criterion for MEG planar gradiometers. The peak-to-peak
+ value of all planar gradiometer signals must exceed this value,
+ for the epoch to be included. This criterion allows rejection of data
+ with saturated or otherwise dysfunctional channels. The default value
+ is zero, *i.e.*, no rejection.
+
+**magFlat <value / T>**
+
+ Signal detection criterion for MEG magnetometers and axial gradiometers
+ channels.
+
+**eegFlat <value / V>**
+
+ Signal detection criterion for EEG channels.
+
+**eogFlat <value / V>**
+
+ Signal detection criterion for EOG channels.
+
+**ecgFlat <value / V>**
+
+ Signal detection criterion for ECG channels.
+
+**stimIgnore <time / s>**
+
+ Ignore this many seconds on both sides of the trigger when considering
+ the epoch. This parameter is useful for ignoring large stimulus artefacts, *e.g.*,
+ from electrical somatosensory stimulation.
+
+**fixSkew**
+
+ Since the sampling of data and the stimulation devices are usually not
+ synchronized, all trigger input bits may not turn on at the same sample.
+ If this option is included in the off-line averaging description
+ file, the following procedure is used to counteract this: if there is
+ a transition from zero to a nonzero value on the digital trigger channel
+ at sample INLINE_EQUATION, the following sample
+ will be checked for a transition from this nonzero value to another
+ nonzero value. If such an event pair is found, the two events will
+ be jointly considered as a transition from zero to the second non-zero
+ value. With the fixSkew option, mne_browse_raw/mne_process_raw behaves
+ like the Elekta-Neuromag on-line averaging and Maxfilter (TM) software.
+
+**name <text>**
+
+ A descriptive name for this set of averages. If the name contains multiple
+ words, enclose it in quotation marks "like this".
+ The name will appear in the average manager window listing in the
+ interactive version of the program and as a comment in the processed
+ data section in the output file.
+
+.. _CACHACHH:
+
+Category definition
+===================
+
+A category (condition) is defined by the parameters listed
+in this section.
+
+**event <number>**
+
+ The zero time point of an epoch to be averaged is defined by a transition
+ from zero to this number on the digital trigger channel. The interpretation
+ of the values on the trigger channel can be further modified by
+ the ignore and mask keywords. If multiple event parameters are present
+ for a category, all specified events will be included in the average.
+
+**ignore <number>**
+
+ If this parameter is specified the selected bits on trigger channel
+ values can be mask (set to zero) out prior to checking for an existence of
+ an event. For example, to ignore the values of trigger input lines three
+ and eight, specify ``ignore 132`` (INLINE_EQUATION).
+
+**mask <number>**
+
+ Works similarly to ignore except that a mask specifies the trigger channel
+ bits to be included. For example, to look at trigger input lines
+ one to three only, ignoring others, specify ``mask 7`` (INLINE_EQUATION)
+
+**prevevent <number>**
+
+ Specifies the event that is required to occur immediately before
+ the event(s) specified with event parameter(s)
+ in order for averaging to occur. Only one previous event number
+ can be specified.
+
+**prevignore <number>**
+
+ Works like ignore but for the
+ events specified with prevevent .
+ If prevignore and prevmask are
+ missing, the mask implied by ignore and mask is
+ applied to prevevent as well.
+
+**prevmask <number>**
+
+ Works like mask but for the events
+ specified with prevevent . If prevignore and prevmask are
+ missing, the mask implied by ignore and mask is
+ applied to prevevent as well.
+
+**nextevent <number>**
+
+ Specifies the event that is required to occur immediately after
+ the event(s) specified with event parameter(s)
+ in order for averaging to occur. Only one next event number can
+ be specified.
+
+**nextignore <number>**
+
+ Works like ignore but for the
+ events specified with nextevent .
+ If nextgnore and nextmask are
+ missing, the mask implied by ignore and mask is
+ applied to nextevent as well.
+
+**nextmask <number>**
+
+ Works like mask but for the events
+ specified with nextevent . If nextignore and nextmask are
+ missing, the mask implied by ignore and mask is
+ applied to nextevent as well.
+
+**delay <time / s>**
+
+ Adds a delay to the time of the occurrence of an event. Therefore,
+ if this parameter is positive, the zero time point of the epoch
+ will be later than the time of the event and, correspondingly, if
+ the parameter is negative, the zero time point of the epoch will
+ be earlier than the event. By default, there will be no delay.
+
+**tmin <time / s>**
+
+ Beginning time point of the epoch.
+
+**tmax <time / s>**
+
+ End time point of the epoch.
+
+**bmin <time / s>**
+
+ Beginning time point of the baseline. If both ``bmin`` and ``bmax`` parameters
+ are present, the baseline defined by this time range is subtracted
+ from each epoch before they are added to the average.
+
+**basemin <time / s>**
+
+ Synonym for bmin.
+
+**bmax <time / s>**
+
+ End time point of the baseline.
+
+**basemax <time / s>**
+
+ Synonym for bmax.
+
+**name <text>**
+
+ A descriptive name for this category. If the name contains multiple words,
+ enclose it in quotation marks "like this". The
+ name will appear in the average manager window listing in the interactive
+ version of the program and as a comment averaging category section
+ in the output file.
+
+**abs**
+
+ Calculate the absolute values of the data in the epoch before adding it to
+ the average.
+
+**stderr**
+
+ The standard error of mean will be computed for this category and included
+ in the output fif file.
+
+.. note:: Specification of the baseline limits does not any more imply the estimation of the standard error of mean. Instead, the stderr parameter is required to invoke this option.
+
+.. _CACEBACG:
+
+Description files for covariance matrix estimation
+##################################################
+
+Covariance matrix estimation is controlled by a another description
+file, very similar to the average definition. A example of a covariance
+description file can be found in the directory ``$MNE_ROOT/share/mne/mne_browse_raw/templates`` .
+
+Overall format
+==============
+
+Any line beginning with the pound sign (#) in this description
+file is a comment. Each parameter in the description file is defined
+by a keyword usually followed by a value. Text values consisting
+of multiple words, separated by spaces, must be included in quotation
+marks. The case of the keywords in the file does not matter. The
+ending ``.cov`` is suggested for the covariance-matrix
+description files.
+
+The general format of the description file is:
+
+``cov {``
+<common parameters>
+``def {``
+<covariance definition parameters>
+``}``
+
+....``}``
+
+The file may contain arbitrarily many covariance definitions,
+starting with ``def`` .
+
+.. warning:: Due to a bug that existed in some versions of the Neuromag acquisition software, the trigger line 8 is incorrectly decoded on trigger channel STI 014. This can be fixed by running mne_fix_stim14 on the raw data file before using mne_browse_raw or mne_process_raw . This bug has been fixed in the acquisition software at the Martinos Center on Nov. 10, 2005.
+
+.. _BABCGEJE:
+
+Common parameters
+=================
+
+The average definition starts with the common parameters.
+They include:
+
+**outfile <name>**
+
+ The name of the file where the covariance matrix is to be stores. This
+ parameter is mandatory.
+
+**eventfile <name>**
+
+ Optional file to contain event specifications. This file can be
+ either in fif or text format (see :ref:`CACBCEGC`). The event
+ file format is recognized from the file name: if it ends with ``.fif`` ,
+ the file is assumed to be in fif format, otherwise a text file is
+ expected. If this parameter is present, the trigger events in the
+ raw data file are ignored and this event file is consulted instead.
+ The event file format is described in :ref:`CACBCEGC`.
+
+**logfile <name>**
+
+ This optional file will contain detailed information about the averaging
+ process. In the interactive mode, the log information can be viewed
+ from the Manage averages window.
+
+**gradReject <value / T/m>**
+
+ Rejection limit for MEG gradiometer channels. If the peak-to-peak amplitude
+ within the extracted epoch exceeds this value on any of the gradiometer
+ channels, the epoch will be omitted from the average.
+
+**magReject <value / T>**
+
+ Rejection limit for MEG magnetometer and axial gradiometer channels.
+ If the peak-to-peak amplitude within the extracted epoch exceeds
+ this value on any of the magnetometer or axial gradiometer channels,
+ the epoch will be omitted from the average.
+
+**eegReject <value / V>**
+
+ Rejection limit for EEG channels. If the peak-to-peak amplitude within
+ the extracted epoch exceeds this value on any of the EEG channels,
+ the epoch will be omitted from the average.
+
+**eogReject <value / V>**
+
+ Rejection limit for EOG channels. If the peak-to-peak amplitude within
+ the extracted epoch exceeds this value on any of the EOG channels,
+ the epoch will be omitted from the average.
+
+**ecgReject <value / V>**
+
+ Rejection limit for ECG channels. If the peak-to-peak amplitude within
+ the extracted epoch exceeds this value on any of the ECG channels,
+ the epoch will be omitted from the average.
+
+**gradFlat <value / T/m>**
+
+ Signal detection criterion for MEG planar gradiometers. The peak-to-peak
+ value of all planar gradiometer signals must exceed this value,
+ for the epoch to be included. This criterion allows rejection of data
+ with saturated or otherwise dysfunctional channels. The default value
+ is zero, *i.e.*, no rejection.
+
+**magFlat <value / T>**
+
+ Signal detection criterion for MEG magnetometers and axial gradiometers
+ channels.
+
+**eegFlat <value / V>**
+
+ Signal detection criterion for EEG channels.
+
+**eogFlat <value / V>**
+
+ Signal detection criterion for EOG channels.
+
+**ecgFlat <value / V>**
+
+ Signal detection criterion for ECG channels.
+
+**stimIgnore <time / s>**
+
+ Ignore this many seconds on both sides of the trigger when considering
+ the epoch. This parameter is useful for ignoring large stimulus artefacts, *e.g.*,
+ from electrical somatosensory stimulation.
+
+**fixSkew**
+
+ Since the sampling of data and the stimulation devices are usually not
+ synchronized, all trigger input bits may not turn on at the same sample.
+ If this option is included in the off-line averaging description
+ file, the following procedure is used to counteract this: if there is
+ a transition from zero to a nonzero value on the digital trigger channel
+ at sample INLINE_EQUATION, the following sample
+ will be checked for a transition from this nonzero value to another
+ nonzero value. If such an event pair is found, the two events will
+ be jointly considered as a transition from zero to the second non-zero
+ value.
+
+**keepsamplemean**
+
+ The means at individual samples will *not* be
+ subtracted in the estimation of the covariance matrix. For details,
+ see :ref:`BABHJDEJ`. This parameter is effective only for
+ estimating the covariance matrix from epochs. It is recommended
+ to specify this option. However, for compatibility with previous
+ MNE releases, keepsamplemean is
+ not on by default.
+
+.. _BABECIAH:
+
+Covariance definitions
+======================
+
+The covariance definitions starting with def specify the
+epochs to be included in the estimation of the covariance matrix.
+
+**event <number>**
+
+ The zero time point of an epoch to be averaged is defined by a transition
+ from zero to this number on the digital trigger channel. The interpretation
+ of the values on the trigger channel can be further modified by
+ the ignore and mask keywords. If multiple event parameters are present
+ in a definition, all specified events will be included. If the event
+ parameter is missing or set to zero, the covariance matrix is computed
+ over a section of the raw data, defined by the ``tmin`` and ``tmax`` parameters.
+
+**ignore <number>**
+
+ If this parameter is specified the selected bits on trigger channel
+ values can be mask (set to zero) out prior to checking for an existence of
+ an event. For example, to ignore the values of trigger input lines three
+ and eight, specify ``ignore 132`` (INLINE_EQUATION).
+
+**mask <number>**
+
+ Works similarly to ignore except that a mask specifies the trigger channel
+ bits to be included. For example, to look at trigger input lines
+ one to three only, ignoring others, specify ``mask 7`` (INLINE_EQUATION)
+
+**delay <time / s>**
+
+ Adds a delay to the time of the occurrence of an event. Therefore,
+ if this parameter is positive, the zero time point of the epoch
+ will be later than the time of the event and, correspondingly, if
+ the parameter is negative, the zero time point of the epoch will
+ be earlier than the time of the event. By default, there will be
+ no delay.
+
+**tmin <time / s>**
+
+ Beginning time point of the epoch. If the ``event`` parameter
+ is zero or missing, this defines the beginning point of the raw
+ data range to be included.
+
+**tmax <time / s>**
+
+ End time point of the epoch. If the ``event`` parameter
+ is zero or missing, this defines the end point of the raw data range
+ to be included.
+
+**bmin <time / s>**
+
+ It is possible to remove a baseline from the epochs before they
+ are included in the covariance matrix estimation. This parameter
+ defines the starting point of the baseline. This feature can be
+ employed to avoid overestimation of noise in the presence of low-frequency drifts.
+ Setting of ``bmin`` and ``bmax`` is always recommended
+ for epoch-based covariance matrix estimation.
+
+**basemin <time / s>**
+
+ Synonym for bmin.
+
+**bmax <time / s>**
+
+ End time point of the baseline, see above.
+
+**basemax <time / s>**
+
+ Synonym for bmax.
+
+.. _CACJFADF:
+
+Managing averages
+#################
+
+This selection pops up a dialog which allows the management
+of computed averages. The controls in the dialog, shown in :ref:`CACEFABD`, allow the following:
+
+- Select which categories (conditions)
+ are displayed in the average view.
+
+- Select the colors of the traces.
+
+- Viewing the log information accumulated in the averaging process.
+
+- Saving of averaged data.
+
+- Setting the active vectors for signal-space projection if
+ the data were loaded from a file.
+
+- Setting the current software gradient compensation for data
+ loaded from a file.
+
+.. _CACEFABD:
+
+.. figure:: picture.png
+ :alt: none
+
+ The dialog for managing available averages.
+
+In the example of :ref:`CACEFABD`, the first item
+is an average computed within mne_browse_raw ,
+the second one contains data loaded from a file with signal-space
+projection data available, the third one demonstrates multiple data
+sets loaded from a file with neither projection nor software gradient
+compensation available, and the last one is a data set loaded from file
+with software gradient compensation data present. Note that this
+is now a scrolled window and some of the loaded data may be below
+or above the current view area.
+
+.. _CACCHABI:
+
+The Signal-Space Projection (SSP) method
+########################################
+
+The Signal-Space Projection (SSP) is one approach to rejection
+of external disturbances in software. The section presents some
+relevant details of this method.
+
+General concepts
+================
+
+Unlike many other noise-cancellation approaches, SSP does
+not require additional reference sensors to record the disturbance
+fields. Instead, SSP relies on the fact that the magnetic field
+distributions generated by the sources in the brain have spatial
+distributions sufficiently different from those generated by external
+noise sources. Furthermore, it is implicitly assumed that the linear
+space spanned by the significant external noise patters has a low
+dimension.
+
+Without loss of generality we can always decompose any INLINE_EQUATION-channel
+measurement INLINE_EQUATION into its signal and
+noise components as
+
+.. math:: 1 + 1 = 2
+
+Further, if we know that INLINE_EQUATION is
+well characterized by a few field patterns INLINE_EQUATION,
+we can express the disturbance as
+
+.. math:: 1 + 1 = 2
+
+where the columns of INLINE_EQUATION constitute
+an orthonormal basis for INLINE_EQUATION, INLINE_EQUATION is
+an INLINE_EQUATION-component column vector, and
+the error term INLINE_EQUATION is small and does
+not exhibit any consistent spatial distributions over time, *i.e.*, INLINE_EQUATION.
+Subsequently, we will call the column space of INLINE_EQUATION the
+noise subspace. The basic idea of SSP is that we can actually find
+a small basis set INLINE_EQUATION such that the
+conditions described above are satisfied. We can now construct the
+orthogonal complement operator
+
+.. math:: 1 + 1 = 2
+
+and apply it to INLINE_EQUATION yielding
+
+.. math:: 1 + 1 = 2
+
+since INLINE_EQUATION. The projection operator INLINE_EQUATION is
+called the signal-space projection operator and generally provides
+considerable rejection of noise, suppressing external disturbances
+by a factor of 10 or more. The effectiveness of SSP depends on two
+factors:
+
+- The basis set INLINE_EQUATION should
+ be able to characterize the disturbance field patterns completely
+ and
+
+- The angles between the noise subspace space spanned by INLINE_EQUATION and the
+ signal vectors INLINE_EQUATION should be as close
+ to INLINE_EQUATION as possible.
+
+If the first requirement is not satisfied, some noise will
+leak through because INLINE_EQUATION. If the any
+of the brain signal vectors INLINE_EQUATION is
+close to the noise subspace not only the noise but also the signal
+will be attenuated by the application of INLINE_EQUATION and,
+consequently, there might by little gain in signal-to-noise ratio. :ref:`CACFGIEC` demonstrates the effect of SSP on the Vectorview
+magnetometer data. After the elimination of a three-dimensional
+noise subspace, the absolute value of the noise is dampened approximately
+by a factor of 10 and the covariance matrix becomes diagonally dominant.
+
+Since the signal-space projection modifies the signal vectors
+originating in the brain, it is necessary to apply the projection
+to the forward solution in the course of inverse computations. This
+is accomplished by mne_inverse_operator as
+described in Section 6.4. For more information on SSP,
+please consult the references listed in Section 13.4.
+
+.. _CACFGIEC:
+
+.. figure:: picture.png
+ :alt: none
+
+ An example of the effect of SSP. The covariance matrix INLINE_EQUATION of noise data on the 102 Vectorview magnetometers was computed (a) before and (b) after the application of SSP with three-dimensional noise subspace. The plotted quantity is INLINE_EQUATION. Note that the vertical scale in (b) is ten times smaller than in (a).
+
+.. _BABFFCHF:
+
+Estimation of the noise subspace
+================================
+
+As described above, application of SSP requires the estimation
+of the signal vectors INLINE_EQUATION constituting
+the noise subspace. The most common approach, also implemented in mne_browse_raw is
+to compute a covariance matrix of empty room data, compute its eigenvalue
+decomposition, and employ the eigenvectors corresponding to the
+highest eigenvalues as basis for the noise subspace. It is also
+customary to use a separate set of vectors for magnetometers and
+gradiometers in the Vectorview system.
+
+EEG average electrode reference
+===============================
+
+In the computation of EEG-based source estimates, the MNE
+software employs the average-electrode reference, which means that
+the average over all electrode signals INLINE_EQUATION is
+subtracted from each INLINE_EQUATION:
+
+.. math:: 1 + 1 = 2
+
+It is easy to see that the above equation actually corresponds
+to the projection:
+
+.. math:: 1 + 1 = 2
+
+where
+
+.. math:: 1 + 1 = 2
+
+.. _CACHAAEG:
+
+Covariance matrix estimation
+############################
+
+This section describes how the covariance matrices are computed
+for raw data and epochs.
+
+Continuous raw data
+===================
+
+If a covariance matrix of a raw data is computed the data
+are checked for artefacts in 200-sample pieces. Let us collect the
+accepted INLINE_EQUATION samples from all channels to
+the vectors INLINE_EQUATION. The estimate of the covariance
+matrix is then computed as:
+
+.. math:: 1 + 1 = 2
+
+where
+
+.. math:: 1 + 1 = 2
+
+is the average of the signals over all times. Note that no
+attempt is made to correct for low frequency drifts in the data.
+If the contribution of any frequency band is not desired in the
+covariance matrix estimate, suitable band-pass filter should be
+applied.
+
+For actual computations, it is convenient to rewrite the
+expression for the covariance matrix as
+
+.. math:: 1 + 1 = 2
+
+.. _BABHJDEJ:
+
+Epochs
+======
+
+The calculation of the covariance matrix is slightly more
+complicated in the epoch mode. If the bmin and bmax parameters
+are specified in the covariance matrix description file (see :ref:`BABECIAH`), baseline correction is first applied to each
+epoch.
+
+Let the vectors
+
+.. math:: 1 + 1 = 2
+
+be the samples from all channels in the baseline corrected epochs
+used to calculate the covariance matrix. In the above, INLINE_EQUATION is
+the number of accepted epochs in category INLINE_EQUATION, INLINE_EQUATION is
+the number of samples in the epochs of category INLINE_EQUATION,
+and INLINE_EQUATION is the number of categories.
+
+If the recommended keepsamplemean option
+is specified in the covariance matrix definition file, the baseline
+correction is applied to the epochs but the means at individual
+samples are not subtracted. Thus the covariance matrix will be computed
+as:
+
+.. math:: 1 + 1 = 2
+
+where
+
+.. math:: 1 + 1 = 2
+
+If keepsamplemean is *not* specified,
+we estimate the covariance matrix as
+
+.. math:: 1 + 1 = 2
+
+where
+
+.. math:: 1 + 1 = 2
+
+and
+
+.. math:: 1 + 1 = 2
+
+which reflects the fact that INLINE_EQUATION means
+are computed for category INLINE_EQUATION. It
+is easy to see that the expression for the covariance matrix estimate
+can be cast into a more convenient form
+
+.. math:: 1 + 1 = 2
+
+Subtraction of the means at individual samples is useful
+if it can be expected that the evoked response from previous stimulus
+extends to part of baseline period of the next one.
+
+Combination of covariance matrix estimates
+==========================================
+
+Let us assume that we have computed multiple covariance matrix
+estimates INLINE_EQUATION with corresponding degrees
+of freedom INLINE_EQUATION. We can combine these
+matrices together as
+
+.. math:: 1 + 1 = 2
+
+where
+
+.. math:: 1 + 1 = 2
+
+SSP information included with covariance matrices
+=================================================
+
+If a signal space projection was on when a covariance matrix
+was calculated, information about the projections applied is included
+with the covariance matrix when it is saved. These projection data
+are read by mne_inverse_operator and
+applied to the forward solution as well as appropriate. Inclusion
+of the projections into the covariance matrix limits the possibilities
+to use the ``--bad`` and ``--proj`` options in mne_inverse_operator ,
+see Section 6.4.
+
+.. _CACGHEGC:
+
+Interacting with mne_analyze
+############################
+
+To facilitate interactive analysis of raw data, mne_browse_raw can
+run mne_analyze as a child process.
+In this mode, mne_analyze is "remote controlled" by mne_browse_raw and
+will also send replies to mne_browse_raw to
+keep the two programs synchronized. A practical application of this
+communication is to view field or potential maps and cortically-constrained
+source estimates computed from raw data instantly.
+
+The subordinate mne_analyze is
+started and stopped from Start mne_analyze and Quit mne_analyze in the Windows menu,
+respectively. The following settings are communicated between the
+two processes:
+
+**The raw data file**
+
+ If a new raw data file is opened and a subordinate mne_analyze is active,
+ the name of the raw data file is communicated to mne_analyze and
+ a simplified version of the open dialog appears in mne_analyze allowing
+ selection of an inverse operator or are MEG/MRI coordinate transformation.
+ If a raw data file is already open in mne_browse_raw when mne_analyze is
+ started, the open dialog appears immediately.
+
+**Time point**
+
+ When a new time point is selected in mne_browse_raw the mne_analyze time
+ point selection is updated accordingly. Time point selection in mne_analyze is
+ not transferred to mne_browse_raw .
+
+**Scales**
+
+ The vertical scales are kept synchronized between the two programs.
+ In addition, the settings of the sample time limits are communicated
+ from mne_browse_raw to mne_analyze .
+
+**Filter**
+
+ The filter settings are kept synchronized.
diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst
new file mode 100644
index 0000000..f698b74
--- /dev/null
+++ b/doc/source/manual/convert.rst
@@ -0,0 +1,2090 @@
+
+
+.. _BEHBBIJF:
+
+===============
+Data conversion
+===============
+
+Overview
+########
+
+This Chapter describes the data conversion utilities included
+with the MNE software.
+
+.. _BEHIAADG:
+
+Importing data from other MEG/EEG systems
+#########################################
+
+This section describes the utilities to convert data from
+other MEG/EEG systems into the fif format.
+
+Importing 4-D Neuroimaging data
+===============================
+
+The newest version of 4-D Magnes software includes the possibility
+to export data in fif. Please consult the documentation of the Magnes
+system for details of this export utility. However, the exported
+fif file does not include information about the compensation channels
+and the weights to be applied to realize software gradient compensation.
+To augment the Magnes fif files with the necessary information,
+the MNE software includes the utilities mne_insert_4D_comp , mne_create_comp_data ,
+and mne_add_to_meas_info.
+
+As a result, the complete 4D Magnes data conversion process
+involves the following steps:
+
+- Export the raw data fif file from the
+ Magnes system.
+
+- If the data comes from a Magnes system where the primary (helmet) sensors
+ are gradiometers instead of magnetometers, run mne_fix_mag_coil_types with
+ the ``--magnes`` option to correct the channel information
+ in the file, see Section 11.4.4.
+
+- Export a text file containing the Magnes compensation sensor
+ data.
+
+- Create a text file containing the appropriate compensation
+ channel weights.
+
+- Run mne_insert_4D_comp with
+ the files created in the first two steps to merge compensation channel
+ data with the original Magnes fif file.
+
+- Run mne_create_comp_data on
+ the file created in step 3. to make a fif file containing the compensation
+ weights.
+
+- Run mne_add_to_meas_info with
+ the fif files created in steps 4. and 5. as input to result in a
+ complete fif file containing all the necessary data.
+
+.. note:: Including the compensation channel data is recommended but not mandatory. If the data are saved in the Magnes system are already compensated, there will be a small error in the forward calculations whose significance has not been evaluated carefully at this time.
+
+.. _BEHDEBCH:
+
+Importing CTF data
+==================
+
+The MNE software includes a utility mne_ctf2fiff ,
+based on the BrainStorm Matlab code by Richard Leahy, John Mosher,
+and Sylvain Baillet, to convert data in CTF ds directory to fif
+format.
+
+The command-line options of mne_ctf2fiff are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---verbose**
+
+ Produce a verbose listing of the conversion process to stdout.
+
+**\---ds <directory>**
+
+ Read the data from this directory
+
+**\---omit <filename>**
+
+ Read the names of channels to be omitted from this text file. Enter one
+ channel name per line. The names should match exactly with those
+ listed in the CTF data structures. By default, all channels are included.
+
+**\---fif <filename>**
+
+ The name of the output file. If the length of the raw data exceeds
+ the 2-GByte fif file limit, several output files will be produced.
+ These additional 'extension' files will be tagged
+ with ``_001.fif`` , ``_002.fif`` , etc.
+
+**\---evoked**
+
+ Produce and evoked-response fif file instead of a raw data file.
+ Each trial in the CTF data file is included as a separate category
+ (condition). The maximum number of samples in each trial is limited
+ to 25000.
+
+**\---infoonly**
+
+ Write only the measurement info to the output file, do not include data.
+
+During conversion, the following files are consulted from
+the ds directory:
+
+**<name> .res4**
+
+ This file contains most of the header information pertaining the acquisition.
+
+**<name> .hc**
+
+ This file contains the HPI coil locations in sensor and head coordinates.
+
+**<name> .meg4**
+
+ This file contains the actual MEG data. If the data are split across several
+ files due to the 2-GByte file size restriction, the 'extension' files
+ are called <name> ``.`` <number> ``_meg4`` .
+
+**<name> .eeg**
+
+ This is an optional input file containing the EEG electrode locations. More
+ details are given below.
+
+If the <name> ``.eeg`` file,
+produced from the Polhemus data file with CTF software, is present,
+it is assumed to contain lines with the format:
+
+<number> <name> <x/cm> <y/cm> <z/cm>
+
+The field <number> is
+a sequential number to be assigned to the converted data point in
+the fif file. <name> is either
+a name of an EEG channel, one of ``left`` , ``right`` ,
+or ``nasion`` to indicate a fiducial landmark, or any word
+which is not a name of any channel in the data. If <name> is
+a name of an EEG channel available in the data, the location is
+included in the Polhemus data as an EEG electrode locations and
+inserted as the location of the EEG electrode. If the name is one
+of the fiducial landmark names, the point is included in the Polhemus
+data as a fiducial landmark. Otherwise, the point is included as
+an additional head surface points.
+
+The standard ``eeg`` file produced by CTF software
+does not contain the fiducial locations. If desired, they can be
+manually copied from the ``pos`` file which was the source
+of the ``eeg`` file.
+
+.. note:: In newer CTF data the EEG position information maybe present in the ``res4`` file. If the ``eeg`` file is present, the positions given there take precedence over the information in the ``res4`` file.
+
+.. note:: mne_ctf2fiff converts both epoch mode and continuous raw data file into raw data fif files. It is not advisable to use epoch mode files with time gaps between the epochs because the data will be discontinuous in the resulting fif file with jumps at the junctions between epochs. These discontinuities produce artefacts if the raw data is filtered in mne_browse_raw , mne_process_raw , or graph .
+
+.. note:: The conversion process includes a transformation from the CTF head coordinate system convention to that used in the Neuromag systems.
+
+.. _BEHBABFA:
+
+Importing CTF Polhemus data
+===========================
+
+The CTF MEG systems store the Polhemus digitization data
+in text files. The utility mne_ctf_dig2fiff was
+created to convert these data files into the fif and hpts formats.
+
+The input data to mne_ctf_dig2fiff is
+a text file, which contains the coordinates of the digitization
+points in centimeters. The first line should contain a single number
+which is the number of points listed in the file. Each of the following
+lines contains a sequential number of the point, followed by the
+three coordinates. mne_ctf_dig2fiff ignores
+any text following the INLINE_EQUATION coordinate
+on each line. If the ``--numfids`` option is specified,
+the first three points indicate the three fiducial locations (1
+= nasion, 2 = left auricular point, 3 = right auricular point).
+Otherwise, the input file must end with three lines beginning with ``left`` , ``right`` ,
+or ``nasion`` to indicate the locations of the fiducial
+landmarks, respectively.
+
+.. note:: The sequential numbers should be unique within a file. I particular, the numbers 1, 2, and 3 must not be appear more than once if the ``--numfids`` options is used.
+
+The command-line options for mne_ctf_dig2fiff are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---dig <name>**
+
+ Specifies the input data file in CTF output format.
+
+**\---numfids**
+
+ Fiducial locations are numbered instead of labeled, see above.
+
+**\---hpts <name>**
+
+ Specifies the output hpts file. The format of this text file is
+ described in :ref:`CJADJEBH`.
+
+**\---fif <name>**
+
+ Specifies the output fif file.
+
+.. _BEHDDFBI:
+
+Applying software gradient compensation
+=======================================
+
+Since the software gradient compensation employed in CTF
+systems is a reversible operation, it is possible to change the
+compensation status of CTF data in the data files as desired. This
+section contains information about the technical details of the
+compensation procedure and a description of mne_compensate_data ,
+which is a utility to change the software gradient compensation
+state in evoked-response data files.
+
+The fif files containing CTF data converted using the utility mne_ctf2fiff contain
+several compensation matrices which are employed to suppress external disturbances
+with help of the reference channel data. The reference sensors are
+located further away from the brain than the helmet sensors and
+are thus measuring mainly the external disturbances rather than magnetic
+fields originating in the brain. Most often, a compensation matrix
+corresponding to a scheme nicknamed *Third-order gradient
+compensation* is employed.
+
+Let us assume that the data contain INLINE_EQUATION MEG
+sensor channels, INLINE_EQUATION reference sensor
+channels, and INLINE_EQUATION other channels.
+The data from all channels can be concatenated into a single vector
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION, INLINE_EQUATION,
+and INLINE_EQUATION are the data vectors corresponding
+to the MEG sensor channels, reference sensor channels, and other
+channels, respectively. The data before and after compensation,
+denoted here by INLINE_EQUATION and INLINE_EQUATION, respectively,
+are related by
+
+.. math:: 1 + 1 = 2
+
+where the composite compensation matrix is
+
+.. math:: 1 + 1 = 2
+
+In the above, INLINE_EQUATION is a INLINE_EQUATION compensation
+data matrix corresponding to compensation "grade" INLINE_EQUATION.
+It is easy to see that
+
+.. math:: 1 + 1 = 2
+
+To convert from compensation grade INLINE_EQUATION to INLINE_EQUATION one
+can simply multiply the inverse of one compensate compensation matrix
+by another and apply the product to the data:
+
+.. math:: 1 + 1 = 2
+
+This operation is performed by mne_compensate_data ,
+which has the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---in <name>**
+
+ Specifies the input data file.
+
+**\---out <name>**
+
+ Specifies the output data file.
+
+**\---grad <number>**
+
+ Specifies the desired compensation grade in the output file. The value
+ can be 1, 2, 3, or 101. The values starting from 101 will be used
+ for 4D Magnes compensation matrices.
+
+.. note:: Only average data is included in the output. Evoked-response data files produced with mne_browse_raw or mne_process_raw may include standard errors of mean, which can not be re-compensated using the above method and are thus omitted.
+
+.. note:: Raw data cannot be compensated using mne_compensate_data . For this purpose, load the data to mne_browse_raw or mne_process_raw , specify the desired compensation grade, and save a new raw data file.
+
+.. _BEHGDDBH:
+
+Importing Magnes compensation channel data
+==========================================
+
+At present, it is not possible to include reference channel
+data to fif files containing 4D Magnes data directly using the conversion
+utilities available for the Magnes systems. However, it is possible
+to export the compensation channel signals in text format and merge
+them with the MEG helmet channel data using mne_insert_4D_comp .
+This utility has the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---in <name>**
+
+ Specifies the input fif file containing the helmet sensor data.
+
+**\---out <name>**
+
+ Specifies the output fif file which will contain both the helmet
+ sensor data and the compensation channel data.
+
+**\---ref <name>**
+
+ Specifies a text file containing the reference sensor data.
+
+Each line of the reference sensor data file contains the
+following information:
+
+**epoch #**
+
+ is
+ always one,
+
+**time/s**
+
+ time point of this sample,
+
+**data/T**
+
+ the reference channel data
+ values.
+
+The standard locations of the MEG (helmet) and compensation
+sensors in a Magnes WH3600 system are listed in ``$MNE_ROOT/share/mne/Magnes_WH3600.pos`` . mne_insert_4D_comp matches
+the helmet sensor positions in this file with those present in the
+input data file and transforms the standard compensation channel
+locations accordingly to be included in the output. Since a standard
+position file is only provided for Magnes WH600, mne_insert_4D_comp only
+works for that type of a system.
+
+The fif files exported from the Magnes systems may contain
+slightly smaller number of samples than originally acquired because
+the total number of samples may not be evenly divisible with a reasonable
+number of samples which will be used as the fif raw data file buffer
+size. Therefore, the reference channel data may contain more samples
+than the fif file. The superfluous samples will be omitted from
+the end.
+
+.. _BEHBIIFF:
+
+Creating software gradient compensation data
+============================================
+
+The utility mne_create_comp_data was
+written to create software gradient compensation weight data for
+4D Magnes fif files. This utility takes a text file containing the
+compensation data as input and writes the corresponding fif file
+as output. This file can be merged into the fif file containing
+4D Magnes data with the utility mne_add_to_meas_info .
+
+The command line options of mne_create_comp_data are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---in <name>**
+
+ Specifies the input text file containing the compensation data.
+
+**\---kind <value>**
+
+ The compensation type to be stored in the output file with the data. This
+ value defaults to 101 for the Magnes compensation and does not need
+ to be changed.
+
+**\---out <name>**
+
+ Specifies the output fif file containing the compensation channel weight
+ matrix INLINE_EQUATION, see :ref:`BEHDDFBI`.
+
+The format of the text-format compensation data file is:
+
+<number of MEG helmet channels> <number of compensation channels included>
+<INLINE_EQUATION> <INLINE_EQUATION>INLINE_EQUATION
+<INLINE_EQUATION> <weights>
+<INLINE_EQUATION> <weights> INLINE_EQUATION
+
+In the above <INLINE_EQUATION> denote
+names of MEG helmet channels and <INLINE_EQUATION>
+those of the compensation channels, respectively. If the channel
+names contain spaces, they must be surrounded by quotes, for example, ``"MEG 0111"`` .
+
+.. _BEHBJGGF:
+
+Importing KIT MEG system data
+=============================
+
+The utility mne_kit2fiff was
+created in collaboration with Alec Maranz and Asaf Bachrach to import
+their MEG data acquired with the 160-channel KIT MEG system to MNE
+software.
+
+To import the data, the following input files are mandatory:
+
+- The Polhemus data file (elp file)
+ containing the locations of the fiducials and the head-position
+ indicator (HPI) coils. These data are usually given in the CTF/4D
+ head coordinate system. However, mne_kit2fiff does
+ not rely on this assumption. This file can be exported directly from
+ the KIT system.
+
+- A file containing the locations of the HPI coils in the MEG
+ device coordinate system. These data are used together with the elp file
+ to establish the coordinate transformation between the head and
+ device coordinate systems. This file can be produced easily by manually
+ editing one of the files exported by the KIT system.
+
+- A sensor data file (sns file)
+ containing the locations and orientations of the sensors. This file
+ can be exported directly from the KIT system.
+
+.. note:: The output fif file will use the Neuromag head coordinate system convention, see Section 5.3. A coordinate transformation between the CTF/4D head coordinates and the Neuromag head coordinates is included. This transformation can be read with MNE Matlab Toolbox routines, see Chapter 10.
+
+The following input files are optional:
+
+- A head shape data file (hsp file)
+ containing locations of additional points from the head surface.
+ These points must be given in the same coordinate system as that
+ used for the elp file and the
+ fiducial locations must be within 1 mm from those in the elp file.
+
+- A raw data file containing the raw data values, sample by
+ sample, as text. If this file is not specified, the output fif file
+ will only contain the measurement info block.
+
+By default mne_kit2fiff includes
+the first 157 channels, assumed to be the MEG channels, in the output
+file. The compensation channel data are not converted by default
+but can be added, together with other channels, with the ``--type`` .
+The channels from 160 onwards are designated as miscellaneous input
+channels (MISC 001, MISC 002, etc.). The channel names and types
+of these channels can be afterwards changed with the mne_rename_channels utility,
+see Section 11.4.5. In addition, it is possible to synthesize
+the digital trigger channel (STI 014) from available analog
+trigger channel data, see the ``--stim`` option, below.
+The synthesized trigger channel data value at sample INLINE_EQUATION will
+be:
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION are the thresholded
+from the input channel data INLINE_EQUATION:
+
+.. math:: 1 + 1 = 2
+
+The threshold value INLINE_EQUATION can
+be adjusted with the ``--stimthresh`` option, see below.
+
+mne_kit2fiff accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---elp <filename>**
+
+ The name of the file containing the locations of the fiducials and
+ the HPI coils. This option is mandatory.
+
+**\---hsp <filename>**
+
+ The name of the file containing the locations of the fiducials and additional
+ points on the head surface. This file is optional.
+
+**\---sns <filename>**
+
+ The name of file containing the sensor locations and orientations. This
+ option is mandatory.
+
+**\---hpi <filename>**
+
+ The name of a text file containing the locations of the HPI coils
+ in the MEG device coordinate frame, given in millimeters. The order of
+ the coils in this file does not have to be the same as that in the elp file.
+ This option is mandatory.
+
+**\---raw <filename>**
+
+ Specifies the name of the raw data file. If this file is not specified, the
+ output fif file will only contain the measurement info block.
+
+**\---sfreq <value/Hz>**
+
+ The sampling frequency of the data. If this option is not specified, the
+ sampling frequency defaults to 1000 Hz.
+
+**\---lowpass <value/Hz>**
+
+ The lowpass filter corner frequency used in the data acquisition.
+ If not specified, this value defaults to 200 Hz.
+
+**\---highpass <value/Hz>**
+
+ The highpass filter corner frequency used in the data acquisition.
+ If not specified, this value defaults to 0 Hz (DC recording).
+
+**\---out <filename>**
+
+ Specifies the name of the output fif format data file. If this file
+ is not specified, no output is produced but the elp , hpi ,
+ and hsp files are processed normally.
+
+**\---stim <chs>**
+
+ Specifies a colon-separated list of numbers of channels to be used
+ to synthesize a digital trigger channel. These numbers refer to
+ the scanning order channels as listed in the sns file,
+ starting from one. The digital trigger channel will be the last
+ channel in the file. If this option is absent, the output file will
+ not contain a trigger channel.
+
+**\---stimthresh <value>**
+
+ The threshold value used when synthesizing the digital trigger channel,
+ see above. Defaults to 1.0.
+
+**\---add <chs>**
+
+ Specifies a colon-separated list of numbers of channels to include between
+ the 157 default MEG channels and the digital trigger channel. These
+ numbers refer to the scanning order channels as listed in the sns file,
+ starting from one.
+
+.. note:: The mne_kit2fiff utility has not been extensively tested yet.
+
+.. _BABHDBBD:
+
+Importing EEG data saved in the EDF, EDF+, or BDF format
+========================================================
+
+Overview
+--------
+
+The mne_edf2fiff allows
+conversion of EEG data from EDF, EDF+, and BDF formats to the fif
+format. Documentation for these three input formats can be found
+at:
+
+**EDF:**
+
+ http://www.edfplus.info/specs/edf.html
+
+**EDF+:**
+
+ http://www.edfplus.info/specs/edfplus.html
+
+**BDF:**
+
+ http://www.biosemi.com/faq/file_format.htm
+
+EDF (European Data Format) and EDF+ are 16-bit formats while
+BDF is a 24-bit variant of this format used by the EEG systems manufactured
+by a company called BioSemi.
+
+None of these formats support electrode location information
+and head shape digitization information. Therefore, this information
+has to be provided separately. Presently hpts and elp file formats
+are supported to include digitization data. For information on these
+formats, see :ref:`CJADJEBH` and http://www.sourcesignal.com/formats_probe.html.
+Note that it is mandatory to have the three fiducial locations (nasion
+and the two auricular points) included in the digitization data.
+Using the locations of the fiducial points the digitization data
+are converted to the MEG head coordinate system employed in the
+MNE software, see Section 5.3. In the comparison of the
+channel names only the intial segment up to the first '-' (dash)
+in the EDF/EDF+/BDF channel name is significant.
+
+The EDF+ files may contain an annotation channel which can
+be used to store trigger information. The Time-stamped Annotation
+Lists (TALs) on the annotation data can be converted to a trigger
+channel (STI 014) using an annotation map file which associates
+an annotation label with a number on the trigger channel. The TALs
+can be listed with the --listtal option,
+see below.
+
+.. warning:: The data samples in a BDF file are represented in a 3-byte (24-bit) format. Since 3-byte raw data buffers are not presently supported in the fif format these data will be changed to 4-byte integers in the conversion. Since the maximum size of a fif file is 2 GBytes, the maximum size of a BDF file to be converted is approximately 1.5 GBytes
+
+.. warning:: The EDF/EDF+/BDF formats support channel dependent sampling rates. This feature is not supported by mne_edf2fiff . However, the annotation channel in the EDF+ format can have a different sampling rate. The annotation channel data is not included in the fif files output.
+
+Using mne_edf2fiff
+------------------
+
+The command-line options of mne_edf2fiff are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---edf <filename>**
+
+ Specifies the name of the raw data file to process.
+
+**\---tal <filename>**
+
+ List the time-stamped annotation list (TAL) data from an EDF+ file here.
+ This output is useful to assist in creating the annotation map file,
+ see the --annotmap option, below.
+ This output file is an event file compatible with mne_browse_raw and mne_process_raw ,
+ see Chapter 4. In addition, in the mapping between TAL
+ labels and trigger numbers provided by the --annotmap option is
+ employed to assign trigger numbers in the event file produced. In
+ the absense of the --annotmap option default trigger number 1024
+ is used.
+
+**\---annotmap <filename>**
+
+ Specify a file which maps the labels of the TALs to numbers on a trigger
+ channel (STI 014) which will be added to the output file if this
+ option is present. This annotation map file
+ may contain comment lines starting with the '%' or '#' characters.
+ The data lines contain a label-number pair, separated by a colon.
+ For example, a line 'Trigger-1:9' means that each
+ annotation labeled with the text 'Trigger-1' will
+ be translated to the number 9 on the trigger channel.
+
+**\---elp <filename>**
+
+ Specifies the name of the an electrode location file. This file
+ is in the "probe" file format used by the *Source
+ Signal Imaging, Inc.* software. For description of the
+ format, see http://www.sourcesignal.com/formats_probe.html. Note
+ that some other software packages may produce electrode-position
+ files with the elp ending not
+ conforming to the above specification. As discussed above, the fiducial
+ marker locations, optional in the "probe" file
+ format specification are mandatory for mne_edf2fiff .
+ When this option is encountered on the command line any previously
+ specified hpts file will be ignored.
+
+**\---hpts <filename>**
+
+ Specifies the name of an electrode position file in the hpts format discussed
+ in :ref:`CJADJEBH`. The mandatory entries are the fiducial marker
+ locations and the EEG electrode locations. It is recommended that
+ electrode (channel) names instead of numbers are used to label the
+ EEG electrode locations. When this option is encountered on the
+ command line any previously specified elp file
+ will be ignored.
+
+**\---meters**
+
+ Assumes that the digitization data in an hpts file
+ is given in meters instead of millimeters.
+
+**\---fif <filename>**
+
+ Specifies the name of the fif file to be output.
+
+Post-conversion tasks
+---------------------
+
+This section outlines additional steps to be taken to use
+the EDF/EDF+/BDF file is converted to the fif format in MNE:
+
+- Some of the channels may not have a
+ digitized electrode location associated with them. If these channels
+ are used for EOG or EMG measurements, their channel types should
+ be changed to the correct ones using the mne_rename_channels utility,
+ see Section 11.4.5. EEG channels which do not have a location
+ associated with them should be assigned to be MISC channels.
+
+- After the channel types are correctly defined, a topographical
+ layout file can be created for mne_browse_raw and mne_analyze using
+ the mne_make_eeg_layout utility,
+ see Section 11.6.
+
+- The trigger channel name in BDF files is "Status".
+ This must be specified with the --digtrig option or with help of
+ the MNE_TRIGGER_CH_NAME environment variable when mne_browse_raw or mne_process_raw is
+ invoked, see Section 4.2.1.
+
+- Only the two least significant bytes on the "Status" channel
+ of BDF files are significant as trigger information the --digtrigmask
+ 0xff option MNE_TRIGGER_CH_MASK environment variable should be used
+ to specify this to mne_browse_raw and mne_process_raw ,
+ see Section 4.2.1.
+
+.. _BEHDGAIJ:
+
+Importing EEG data saved in the Tufts University format
+=======================================================
+
+The utility mne_tufts2fiff was
+created in collaboration with Phillip Holcomb and Annette Schmid
+from Tufts University to import their EEG data to the MNE software.
+
+The Tufts EEG data is included in three files:
+
+- The raw data file containing the acquired
+ EEG data. The name of this file ends with the suffix ``.raw`` .
+
+- The calibration raw data file. This file contains known calibration
+ signals and is required to bring the data to physical units. The
+ name of this file ends with the suffix ``c.raw`` .
+
+- The electrode location information file. The name of this
+ file ends with the suffix ``.elp`` .
+
+The utility mne_tufts2fiff has
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---raw <filename>**
+
+ Specifies the name of the raw data file to process.
+
+**\---cal <filename>**
+
+ The name of the calibration data file. If calibration data are missing, the
+ calibration coefficients will be set to unity.
+
+**\---elp <filename>**
+
+ The name of the electrode location file. If this file is missing,
+ the electrode locations will be unspecified. This file is in the "probe" file
+ format used by the *Source Signal Imaging, Inc.* software.
+ For description of the format, see http://www.sourcesignal.com/formats_probe.html.
+ The fiducial marker locations, optional in the "probe" file
+ format specification are mandatory for mne_tufts2fiff . Note
+ that some other software packages may produce electrode-position
+ files with the elp ending not
+ conforming to the above specification.
+
+.. note:: The conversion process includes a transformation from the Tufts head coordinate system convention to that used in the Neuromag systems.
+
+.. note:: The fiducial landmark locations, optional in the probe file format, must be present for mne_tufts2fiff .
+
+.. _BEHCCCDC:
+
+Importing BrainVision EEG data
+==============================
+
+The utility mne_brain_vision2fiff was
+created to import BrainVision EEG data. This utility also helps
+to import the eXimia (Nexstim) TMS-compatible EEG system data to
+the MNE software. The utility uses an optional fif file containing
+the head digitization data to allow source modeling. The MNE Matlab
+toolbox contains the function fiff_write_dig_file to
+write a digitization file based on digitization data available in
+another format, see Chapter 10.
+
+The command-line options of mne_brain_vision2fiff are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---header <name>**
+
+ The name of the BrainVision header file. The extension of this file
+ is ``vhdr`` . The header file typically refers to a marker
+ file (``vmrk`` ) which is automatically processed and a
+ digital trigger channel (STI 014) is formed from the marker information.
+ The ``vmrk`` file is ignored if the ``--eximia`` option
+ is present.
+
+**\---dig <name>**
+
+ The name of the fif file containing the digitization data.
+
+**\---orignames**
+
+ Use the original EEG channel labels. If this option is absent the EEG
+ channels will be automatically renamed to EEG 001, EEG 002, *etc.*
+
+**\---eximia**
+
+ Interpret this as an eXimia data file. The first three channels
+ will be thresholded and interpreted as trigger channels. The composite
+ digital trigger channel will be composed in the same way as in the mne_kit2fiff utility,
+ see :ref:`BEHBJGGF`, above. In addition, the fourth channel
+ will be assigned as an EOG channel. This option is normally used
+ by the mne_eximia2fiff script,
+ see :ref:`BEHGCEHH`.
+
+**\---split <size/MB>**
+
+ Split the output data into several files which are no more than <size> MB.
+ By default, the output is split into files which are just below
+ 2 GB so that the fif file maximum size is not exceeded.
+
+**\---out <filename>**
+
+ Specifies the name of the output fif format data file. If <filename> ends
+ with ``.fif`` or ``_raw.fif`` , these endings are
+ deleted. After these modifications, ``_raw.fif`` is inserted
+ after the remaining part of the file name. If the file is split
+ into multiple parts, the additional parts will be called <name> ``-`` <number> ``_raw.fif`` .
+
+.. _BEHGCEHH:
+
+Converting eXimia EEG data
+==========================
+
+EEG data from the Nexstim eXimia system can be converted
+to the fif format with help of the mne_eximia2fiff script.
+It creates a BrainVision ``vhdr`` file and calls mne_brain_vision2fiff .
+Usage:
+
+``mne_eximia2fiff`` [--dig dfile ] [``--orignames`` ] file1 file2 ...
+
+where file1 file2 ...
+are eXimia ``nxe`` files and the ``--orignames`` option
+is passed on to mne_brain_vision2fiff .
+If you want to convert all data files in a directory, say
+
+``mne_eximia2fiff nxe``
+
+The optional file specified with the --dig option is assumed
+to contain digitizer data from the recording in the Nexstim format.
+The resulting fif data file will contain these data converted to
+the fif format as well as the coordinate transformation between
+the eXimia digitizer and MNE head coordinate systems.
+
+.. note:: This script converts raw data files only.
+
+.. _BABCJEAD:
+
+Converting digitization data
+############################
+
+The mne_convert_dig_data utility
+converts Polhemus digitization data between different file formats.
+The input formats are:
+
+**fif**
+
+ The
+ standard format used in MNE. The digitization data are typically
+ present in the measurement files.
+
+**hpts**
+
+ A text format which is a translation
+ of the fif format data, see :ref:`CJADJEBH` below.
+
+**elp**
+
+ A text format produced by the *Source
+ Signal Imaging, Inc.* software. For description of this "probe" format,
+ see http://www.sourcesignal.com/formats_probe.html.
+
+The data can be output in fif and hpts formats.
+Only the last command-line option specifying an input file will
+be honored. Zero or more output file options can be present on the
+command line.
+
+.. note:: The elp and hpts input files may contain textual EEG electrode labels. They will not be copied to the fif format output.
+
+The command-line options of mne_convert_dig_data are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---fif <name>**
+
+ Specifies the name of an input fif file.
+
+**\---hpts <name>**
+
+ Specifies the name of an input hpts file.
+
+**\---elp <name>**
+
+ Specifies the name of an input elp file.
+
+**\---fifout <name>**
+
+ Specifies the name of an output fif file.
+
+**\---hptsout <name>**
+
+ Specifies the name of an output hpts file.
+
+**\---headcoord**
+
+ The fif and hpts input
+ files are assumed to contain data in the MNE head coordinate system,
+ see Section 5.3. With this option present, the data are
+ transformed to the MNE head coordinate system with help of the fiducial
+ locations in the data. Use this option if this is not the case or
+ if you are unsure about the definition of the coordinate system
+ of the fif and hpts input
+ data. This option is implied with elp input
+ files. If this option is present, the fif format output file will contain
+ the transformation between the original digitizer data coordinates
+ the MNE head coordinate system.
+
+.. _CJADJEBH:
+
+The hpts format
+===============
+
+The hpts format digitzer
+data file may contain comment lines starting with the pound sign
+(#) and data lines of the form:
+
+<category> <identifier> <x/mm> <y/mm> <z/mm>
+
+where
+
+**<category>**
+
+ defines the type of points. Allowed categories are: hpi , cardinal (fiducial ),eeg ,
+ and extra corresponding to head-position
+ indicator coil locations, cardinal landmarks, EEG electrode locations,
+ and additional head surface points, respectively. Note that tkmedit does not
+ recognize the fiducial as an
+ alias for cardinal .
+
+**<identifier>**
+
+ identifies the point. The identifiers are usually sequential numbers. For
+ cardinal landmarks, 1 = left auricular point, 2 = nasion, and 3
+ = right auricular point. For EEG electrodes, identifier = 0 signifies
+ the reference electrode. Some programs (not tkmedit )
+ accept electrode labels as identifiers in the eeg category.
+
+**<x/mm> , <y/mm> , <z/mm>**
+
+ Location of the point, usually in the MEG head coordinate system, see Section 5.3.
+ Some programs have options to accept coordinates in meters instead
+ of millimeters. With --meters option, mne_transform_points lists
+ the coordinates in meters.
+
+.. _BEHDEJEC:
+
+Converting volumetric data into an MRI overlay
+##############################################
+
+With help of the mne_volume_source_space utility
+(Section 5.5) it is possible to create a source space which
+is defined within a volume rather than a surface. If the ``--mri`` option
+was used in mne_volume_source_space , the
+source space file contains an interpolator matrix which performs
+a trilinear interpolation into the voxel space of the MRI volume
+specified.
+
+At present, the MNE software does not include facilities
+to compute volumetric source estimates. However, it is possible
+to calculate forward solutions in the volumetric grid and use the
+MNE Matlab toolbox to read the forward solution. It is then possible
+to compute, *e.g.*, volumetric beamformer solutions
+in Matlab and output the results into w or stc files.
+The purpose of the mne_volume_data2mri is
+to produce MRI overlay data compatible with FreeSurfer MRI viewers
+(in the mgh or mgz formats) from this type of w or stc files.
+
+mne_volume_data2mri accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---src <filename>**
+
+ The name of the volumetric source space file created with mne_volume_source_space .
+ The source space must have been created with the ``--mri`` option,
+ which adds the appropriate sparse trilinear interpolator matrix
+ to the source space.
+
+**\---w <filename>**
+
+ The name of a w file to convert
+ into an MRI overlay.
+
+**\---stc <filename>**
+
+ The name of the stc file to convert
+ into an MRI overlay. If this file has many time frames, the output
+ file may be huge. Note: If both ``-w`` and ``--stc`` are
+ specified, ``-w`` takes precedence.
+
+**\---scale <number>**
+
+ Multiply the stc or w by
+ this scaling constant before producing the overlay.
+
+**\---out <filename>**
+
+ Specifies the name of the output MRI overlay file. The name must end
+ with either ``.mgh`` or ``.mgz`` identifying the
+ uncompressed and compressed FreeSurfer MRI formats, respectively.
+
+.. _BEHBHIDH:
+
+Listing source space data
+#########################
+
+The utility mne_list_source_space outputs
+the source space information into text files suitable for loading
+into the Neuromag MRIlab software.
+
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---src <name>**
+
+ The source space to be listed. This can be either the output from mne_make_source_space
+ \src.fif), output from the forward calculation \fwd.fif), or
+ the output from the inverse operator decomposition \inv.fif).
+
+**\---mri <name>**
+
+ A file containing the transformation between the head and MRI coordinates
+ is specified with this option. This file can be either a Neuromag
+ MRI description file, the output from the forward calculation \fwd.fif),
+ or the output from the inverse operator decomposition \inv.fif).
+ If this file is included, the output will be in head coordinates.
+ Otherwise the source space will be listed in MRI coordinates.
+
+**\---dip <name>**
+
+ Specifies the 'stem' for the Neuromag text format
+ dipole files to be output. Two files will be produced: <stem> -lh.dip
+ and <stem> -rh.dip. These correspond
+ to the left and right hemisphere part of the source space, respectively.
+ This source space data can be imported to MRIlab through the File/Import/Dipoles menu
+ item.
+
+**\---pnt <name>**
+
+ Specifies the 'stem' for Neuromag text format
+ point files to be output. Two files will be produced: <stem> -lh.pnt
+ and <stem> -rh.pnt. These correspond
+ to the left and right hemisphere part of the source space, respectively.
+ This source space data can be imported to MRIlab through the File/Import/Strings menu
+ item.
+
+**\---exclude <name>**
+
+ Exclude the source space points defined by the given FreeSurfer 'label' file
+ from the output. The name of the file should end with ``-lh.label``
+ if it refers to the left hemisphere and with ``-rh.label`` if
+ it lists points in the right hemisphere, respectively.
+
+**\---include <name>**
+
+ Include only the source space points defined by the given FreeSurfer 'label' file
+ to the output. The file naming convention is the same as described
+ above under the ``--exclude`` option. Are 'include' labels are
+ processed before the 'exclude' labels.
+
+**\---all**
+
+ Include all nodes in the output files instead of only those active
+ in the source space. Note that the output files will be huge if
+ this option is active.
+
+.. _BEHBBEHJ:
+
+Listing BEM mesh data
+#####################
+
+The utility mne_list_bem outputs
+the BEM meshes in text format. The default output data contains
+the *x*, *y*, and *z* coordinates
+of the vertices, listed in millimeters, one vertex per line.
+
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---bem <name>**
+
+ The BEM file to be listed. The file name normally ends with -bem.fif or -bem-sol.fif .
+
+**\---out <name>**
+
+ The output file name.
+
+**\---id <number>**
+
+ Identify the surface to be listed. The surfaces are numbered starting with
+ the innermost surface. Thus, for a three-layer model the surface numbers
+ are: 4 = scalp, 3 = outer skull, 1 = inner skull
+ Default value is 4.
+
+**\---gdipoli**
+
+ List the surfaces in the format required by Thom Oostendorp's
+ gdipoli program. This is also the default input format for mne_surf2bem .
+
+**\---meters**
+
+ List the surface coordinates in meters instead of millimeters.
+
+**\---surf**
+
+ Write the output in the binary FreeSurfer format.
+
+**\---xfit**
+
+ Write a file compatible with xfit. This is the same effect as using
+ the options ``--gdipoli`` and ``--meters`` together.
+
+.. _BEHDIAJG:
+
+Converting surface data between different formats
+#################################################
+
+The utility mne_convert_surface converts
+surface data files between different formats.
+
+.. note:: The MNE Matlab toolbox functions enable reading of FreeSurfer surface files directly. Therefore, the --mat option has been removed. The dfs file format conversion functionality has been moved here from mne_convert_dfs . Consequently, mne_convert_dfs has been removed from MNE software.
+
+.. _BABEABAA:
+
+command-line options
+====================
+
+mne_convert_surface accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---fif <name>**
+
+ Specifies a fif format input file. The first surface (source space)
+ from this file will be read.
+
+**\---tri <name>**
+
+ Specifies a text format input file. The format of this file is described in Section 5.6.3.
+
+**\---meters**
+
+ The unit of measure for the vertex locations in a text input files
+ is meters instead of the default millimeters. This option does not
+ have any effect on the interpretation of the FreeSurfer surface
+ files specified with the ``--surf`` option.
+
+**\---swap**
+
+ Swap the ordering or the triangle vertices. The standard convention in
+ the MNE software is to have the vertices in text format files ordered
+ so that the vector cross product of the vectors from vertex 1 to
+ 2 and 1 to 3 gives the direction of the outward surface normal. This
+ is also called the counterclockwise ordering. If your text input file
+ does not comply with this right-hand rule, use the ``--swap`` option.
+ This option does not have any effect on the interpretation of the FreeSurfer surface
+ files specified with the ``--surf`` option.
+
+**\---surf <name>**
+
+ Specifies a FreeSurfer format
+ input file.
+
+**\---dfs <name>**
+
+ Specifies the name of a dfs file to be converted. The surfaces produced
+ by BrainSuite are in the dfs format.
+
+**\---mghmri <name>**
+
+ Specifies a mgh/mgz format MRI data file which will be used to define
+ the coordinate transformation to be applied to the data read from
+ a dfs file to bring it to the FreeSurfer MRI
+ coordinates, *i.e.*, the coordinate system of
+ the MRI stack in the file. In addition, this option can be used
+ to insert "volume geometry" information to the FreeSurfer
+ surface file output (--surfout option). If the input file already
+ contains the volume geometry information, --replacegeom is needed
+ to override the input volume geometry and to proceed to writing
+ the data.
+
+**\---replacegeom**
+
+ Replaces existing volume geometry information. Used in conjunction
+ with the --mghmri option described above.
+
+**\---fifmri <name>**
+
+ Specifies a fif format MRI destription file which will be used to define
+ the coordinate transformation to be applied to the data read from
+ a dfs file to bring it to the same coordinate system as the MRI stack
+ in the file.
+
+**\---trans <name>**
+
+ Specifies the name of a text file which contains the coordinate
+ transformation to be applied to the data read from the dfs file
+ to bring it to the MRI coordinates, see below. This option is rarely
+ needed.
+
+**\---flip**
+
+ By default, the dfs surface nodes are assumed to be in a right-anterior-superior
+ (RAS) coordinate system with its origin at the left-posterior-inferior
+ (LPI) corner of the MRI stack. Sometimes the dfs file has left and
+ right flipped. This option reverses this flip, *i.e.*,
+ assumes the surface coordinate system is left-anterior-superior
+ (LAS) with its origin in the right-posterior-inferior (RPI) corner
+ of the MRI stack.
+
+**\---shift <value/mm>**
+
+ Shift the surface vertices to the direction of the surface normals
+ by this amount before saving the surface.
+
+**\---surfout <name>**
+
+ Specifies a FreeSurfer format output file.
+
+**\---fifout <name>**
+
+ Specifies a fif format output file.
+
+**\---triout <name>**
+
+ Specifies an ASCII output file that will contain the surface data
+ in the triangle file format desribed in Section 5.6.3.
+
+**\---pntout <name>**
+
+ Specifies a ASCII output file which will contain the vertex numbers only.
+
+**\---metersout**
+
+ With this option the ASCII output will list the vertex coordinates
+ in meters instead of millimeters.
+
+**\---swapout**
+
+ Defines the vertex ordering of ASCII triangle files to be output.
+ For details, see ``--swap`` option, above.
+
+**\---smfout <name>**
+
+ Specifies a smf (Simple Model Format) output file. For details of this
+ format, see http://people.scs.fsu.edu/~burkardt/data/smf.txt.
+
+.. note:: Multiple output options can be specified to produce outputs in several different formats with a single invocation of mne_convert_surface .
+
+The coordinate transformation file specified with the ``--trans`` should contain
+a 4 x 4 coordinate transformation matrix:
+
+.. math:: 1 + 1 = 2
+
+defined so that if the augmented location vectors in the
+dfs file and MRI coordinate systems are denoted by INLINE_EQUATION and INLINE_EQUATION,
+respectively,
+
+.. math:: 1 + 1 = 2
+
+.. _BABBHHHE:
+
+Converting MRI data into the fif format
+#######################################
+
+The utility mne_make_cor_set creates
+a fif format MRI description
+file optionally including the MRI data using FreeSurfer MRI volume
+data as input. The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---dir <directory>**
+
+ Specifies a directory containing the MRI volume in COR format. Any
+ previous ``--mgh`` options are cancelled when this option
+ is encountered.
+
+**\---withdata**
+
+ Include the pixel data to the output file. This option is implied
+ with the ``--mgh`` option.
+
+**\---mgh <name>**
+
+ An MRI volume volume file in mgh or mgz format.
+ The ``--withdata`` option is implied with this type of
+ input. Furthermore, the INLINE_EQUATION transformation,
+ the Talairach transformation INLINE_EQUATION from
+ the talairach.xfm file referred to in the MRI volume, and the the
+ fixed transforms INLINE_EQUATION and INLINE_EQUATION will
+ added to the output file. For definition of the coordinate transformations,
+ see Section 5.2.
+
+**\---talairach <name>**
+
+ Take the Talairach transform from this file instead of the one specified
+ in mgh/mgz files.
+
+**\---out <name>**
+
+ Specifies the output file, which is a fif-format MRI description
+ file.
+
+.. _BABBIFIJ:
+
+Collecting coordinate transformations into one file
+###################################################
+
+The utility mne_collect_transforms collects
+coordinate transform information from various sources and saves
+them into a single fif file. The coordinate transformations used
+by MNE software are summarized in Figure 5.1. The output
+of mne_collect_transforms may
+include all transforms referred to therein except for the sensor
+coordinate system transformations INLINE_EQUATION.
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---meas <name>**
+
+ Specifies a measurement data file which provides INLINE_EQUATION.
+ A forward solution or an inverse operator file can also be specified
+ as implied by Table 5.1.
+
+**\---mri <name>**
+
+ Specifies an MRI description or a standalone coordinate transformation
+ file produced by mne_analyze which
+ provides INLINE_EQUATION. If the ``--mgh`` option
+ is not present mne_collect_transforms also
+ tries to find INLINE_EQUATION, INLINE_EQUATION, INLINE_EQUATION,
+ and INLINE_EQUATION from this file.
+
+**\---mgh <name>**
+
+ An MRI volume volume file in mgh or mgz format.
+ This file provides INLINE_EQUATION. The transformation INLINE_EQUATION will
+ be read from the talairach.xfm file referred to in the MRI volume.
+ The fixed transforms INLINE_EQUATION and INLINE_EQUATIONwill
+ be also created.
+
+**\---out <name>**
+
+ Specifies the output file. If this option is not present, the collected transformations
+ will be output on screen but not saved.
+
+.. _BEHCHGHD:
+
+Converting an ncov covariance matrix file to fiff
+#################################################
+
+The ncov file format was used to store the noise-covariance
+matrix file. The MNE software requires that the covariance matrix
+files are in fif format. The utility mne_convert_ncov converts
+ncov files to fif format.
+
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---ncov <name>**
+
+ The ncov file to be converted.
+
+**\---meas <name>**
+
+ A fif format measurement file used to assign channel names to the noise-covariance
+ matrix elements. This file should have precisely the same channel
+ order within MEG and EEG as the ncov file. Typically, both the ncov
+ file and the measurement file are created by the now mature off-line
+ averager, meg_average .
+
+.. _BEHCDBHG:
+
+Converting a lisp covariance matrix to fiff
+###########################################
+
+The utility mne_convert_lspcov converts a LISP-format noise-covariance file,
+produced by the Neuromag signal processor, graph into fif format.
+
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---lspcov <name>**
+
+ The LISP noise-covariance matrix file to be converted.
+
+**\---meas <name>**
+
+ A fif format measurement file used to assign channel names to the noise-covariance
+ matrix elements. This file should have precisely the same channel
+ order within MEG and EEG as the LISP-format covariance matrix file.
+
+**\---out <name>**
+
+ The name of a fif format output file. The file name should end with
+ -cov.fif.text format output file. No information about the channel names
+ is included. The covariance matrix file is listed row by row. This
+ file can be loaded to MATLAB, for example
+
+**\---outasc <name>**
+
+ The name of a text format output file. No information about the channel
+ names is included. The covariance matrix file is listed row by row.
+ This file can be loaded to MATLAB, for example
+
+.. _BEHCCEBJ:
+
+The MNE data file conversion tool
+#################################
+
+This utility, called mne_convert_mne_data ,
+allows the conversion of various fif files related to the MNE computations
+to other formats. The two principal purposes of this utility are
+to facilitate development of new analysis approaches with Matlab
+and conversion of the forward model and noise covariance matrix
+data into evoked-response type fif files, which can be accessed
+and displayed with the Neuromag source modelling software.
+
+.. note:: Most of the functions of mne_convert_mne_data are now covered by the MNE Matlab toolbox covered in Chapter 10. This toolbox is recommended to avoid creating additional files occupying disk space.
+
+.. _BEHCICCF:
+
+Command-line options
+====================
+
+The command-line options recognize
+by mne_convert_mne_data are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---fwd <name>**
+
+ Specity the name of the forward solution file to be converted. Channels
+ specified with the ``--bad`` option will be excluded from
+ the file.
+
+**\---fixed**
+
+ Convert the forward solution to the fixed-orientation mode before outputting
+ the converted file. With this option only the field patterns corresponding
+ to a dipole aligned with the estimated cortex surface normal are
+ output.
+
+**\---surfsrc**
+
+ When outputting a free-orientation forward model (three orthogonal dipole
+ components present) rotate the dipole coordinate system at each
+ source node so that the two tangential dipole components are output
+ first, followed by the field corresponding to the dipole aligned
+ with the estimated cortex surface normal. The orientation of the
+ first two dipole components in the tangential plane is arbitrarily selected
+ to create an orthogonal coordinate system.
+
+**\---noiseonly**
+
+ When creating a 'measurement' fif file, do not
+ output a forward model file, just the noise-covariance matrix.
+
+**\---senscov <name>**
+
+ Specifies the fif file containing a sensor covariance matrix to
+ be included with the output. If no other input files are specified
+ only the covariance matrix is output
+
+**\---srccov <name>**
+
+ Specifies the fif file containing the source covariance matrix to
+ be included with the output. Only diagonal source covariance files
+ can be handled at the moment.
+
+**\---bad <name>**
+
+ Specifies the name of the file containing the names of the channels to
+ be omitted, one channel name per line. This does not affect the output
+ of the inverse operator since the channels have been already selected
+ when the file was created.
+
+**\---fif**
+
+ Output the forward model and the noise-covariance matrix into 'measurement' fif
+ files. The forward model files are tagged with <modalities> ``-meas-fwd.fif`` and
+ the noise-covariance matrix files with <modalities> ``-meas-cov.fif`` .
+ Here, modalities is ``-meg`` if MEG is included, ``-eeg`` if
+ EEG is included, and ``-meg-eeg`` if both types of signals
+ are present. The inclusion of modalities is controlled by the ``--meg`` and ``--eeg`` options.
+
+**\---mat**
+
+ Output the data into MATLAB mat files. This is the default. The
+ forward model files are tagged with <modalities> ``-fwd.mat`` forward model
+ and noise-covariance matrix output, with ``-inv.mat`` for inverse
+ operator output, and with ``-inv-meas.mat`` for combined inverse
+ operator and measurement data output, respectively. The meaning
+ of <modalities> is the same
+ as in the fif output, described above.
+
+**\---tag <name>**
+
+ By default, all variables in the matlab output files start with
+ MNE_. This option allows to change this prefix to <name> _.
+
+**\---meg**
+
+ Include MEG channels from the forward solution and noise-covariance
+ matrix.
+
+**\---eeg**
+
+ Include EEG channels from the forward solution and noise-covariance
+ matrix.
+
+**\---inv <name>**
+
+ Output the inverse operator data from the specified file into a
+ mat file. The source and noise covariance matrices as well as active channels
+ have been previously selected when the inverse operator was created
+ with mne_inverse_operator . Thus
+ the options ``--meg`` , ``--eeg`` , ``--senscov`` , ``--srccov`` , ``--noiseonly`` ,
+ and ``--bad`` do not affect the output of the inverse operator.
+
+**\---meas <name>**
+
+ Specifies the file containing measurement data to be output together with
+ the inverse operator. The channels corresponding to the inverse operator
+ are automatically selected from the file if ``--inv`` .
+ option is present. Otherwise, the channel selection given with ``--sel`` option will
+ be taken into account.
+
+**\---set <number>**
+
+ Select the data set to be output from the measurement file.
+
+**\---bmin <value/ms>**
+
+ Specifies the baseline minimum value setting for the measurement signal
+ output.
+
+**\---bmax <value/ms>**
+
+ Specifies the baseline maximum value setting for the measurement signal
+ output.
+
+.. note:: The ``--tmin`` and ``--tmax`` options which existed in previous versions of mne_converted_mne_data have been removed. If output of measurement data is requested, the entire averaged epoch is now included.
+
+Guide to combining options
+==========================
+
+The combination of options is quite complicated. The :ref:`BEHDCIII` should be helpful to determine the combination
+of options appropriate for your needs.
+
+.. _BEHDCIII:
+
+.. table:: Guide to combining mne_convert_mne_data options.
+
+ ============================================ ======== ===================================================================================== ===============================
+ Desired output Format Required options Optional options
+ ============================================ ======== ===================================================================================== ===============================
+ forward model fif --fwd <name> --out <name> --meg and/or --eeg --fif --bad <name> --surfsrc
+ forward model mat --fwd <name> --out <name> --meg and/or --eeg --bad <name> --surfsrc
+ forward model and sensor covariance mat --fwd <name> --out <name> --senscov <name> --meg and/or --eeg --bad <name> --surfsrc
+ sensor covariance fif --fwd <name> --out <name> --senscov <name> --noiseonly --fif --meg and/or --eeg --bad <name>
+ sensor covariance mat --senscov <name> --out <name --bad <name>
+ sensor covariance eigenvalues text --senscov <name> --out <name --eig --bad <name>
+ evoked MEG/EEG data mat --meas <name> --out <name --sel <name> --set <number>
+ evoked MEG/EEG data forward model mat --meas <name> --fwd <name> --out <name> --bad <name> --set <number>
+ inverse operator data mat --inv <name> --out <name
+ inverse operator data evoked MEG/EEG data mat --inv <name> --meas <name> --out <name
+ ============================================ ======== ===================================================================================== ===============================
+
+Matlab data structures
+======================
+
+The Matlab output provided by mne_convert_mne_data is
+organized in structures, listed in :ref:`BEHCICCA`. The fields
+occurring in these structures are listed in :ref:`BABCBIGF`.
+
+The symbols employed in variable size descriptions are:
+
+**nloc**
+
+ Number
+ of source locations
+
+**nsource**
+
+ Number
+ of sources. For fixed orientation sources nsource = nloc whereas nsource = 3*nloc for
+ free orientation sources
+
+**nchan**
+
+ Number
+ of measurement channels.
+
+**ntime**
+
+ Number
+ of time points in the measurement data.
+
+.. _BEHCICCA:
+
+.. table:: Matlab structures produced by mne_convert_mne_data . The prefix given with the --tag option is indicated <tag> , see :ref:`BEHCICCF`. Its default value is MNE.
+
+ =============== =======================================
+ Structure Contents
+ =============== =======================================
+ <tag> _meas Measured data
+ <tag> _inv The inverse operator decomposition
+ <tag> _fwd The forward solution
+ <tag> _noise A standalone noise-covariance matrix
+ =============== =======================================
+
+.. _BABCBIGF:
+
+.. table:: The fields of Matlab structures.
+
+ =================== ================== =============================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+ Variable Size Description
+ =================== ================== =============================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+ fwd nsource x nchan The forward solution, one source on each row. For free orientation sources, the fields of the three orthogonal dipoles for each location are listed consecutively.
+ names ch_names nchan (string) String array containing the names of the channels included
+ ch_types nchan x 2 The column lists the types of the channels (1 = MEG, 2 = EEG). The second column lists the coil types, see Tables 5.2 and 5.3. For EEG electrodes, this value equals one.
+ ch_pos nchan x 3 The location information for each channel. The first three values specify the origin of the sensor coordinate system or the location of the electrode. For MEG channels, the following nine number specify the *x*, *y*, and *z*-direction unit vectors of the sensor coordinate system. For EEG electrodes the first unit vector specifies the location of the reference electrode. If the reference is not specified this value is all zeroes. The remaining [...]
+ ch_lognos nchan x 1 Logical channel numbers as listed in the fiff file
+ ch_units nchan x 2 Units and unit multipliers as listed in the fif file. The unit of the data is listed in the first column (T = 112, T/m = 201, V = 107). At present, the second column will be always zero, *i.e.*, no unit multiplier.
+ ch_cals nchan x 2 Even if the data comes from the conversion already calibrated, the original calibration factors are included. The first column is the range member of the fif data structures and while the second is the cal member. To get calibrated values in the units given in ch_units from the raw data, the data must be multiplied with the product of range and cal .
+ sfreq 1 The sampling frequency in Hz.
+ lowpass 1 Lowpass filter frequency (Hz)
+ highpass 1 Highpass filter frequency (Hz)
+ source_loc nloc x 3 The source locations given in the coordinate frame indicated by the coord_frame member.
+ source_ori nsource x 3 The source orientations
+ source_selection nsource x 2 Indication of the sources selected from the complete source spaces. Each row contains the number of the source in the complete source space (starting with 0) and the source space number (1 or 2). These numbers refer to the order the two hemispheres where listed when mne_make_source_space was invoked. mne_setup_source_space lists the left hemisphere first.
+ coord_frame string Name of the coordinate frame employed in the forward calculations. Possible values are 'head' and 'mri'.
+ mri_head_trans 4 x 4 The coordinate frame transformation from mri the MEG 'head' coordinates.
+ meg_head_trans 4 x 4 The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates
+ noise_cov nchan x nchan The noise covariance matrix
+ source_cov nsource The elements of the diagonal source covariance matrix.
+ sing nchan The singular values of INLINE_EQUATION with INLINE_EQUATION selected so that INLINE_EQUATION as discussed in Section 6.2.3
+ eigen_fields nchan x nchan The rows of this matrix are the left singular vectors of INLINE_EQUATION, i.e., the columns of INLINE_EQUATION, see above.
+ eigen_leads nchan x nsource The rows of this matrix are the right singular vectors of INLINE_EQUATION, i.e., the columns of INLINE_EQUATION, see above.
+ noise_eigenval nchan In terms of Section 6.2.3, eigenvalues of INLINE_EQUATION, i.e., not scaled with number of averages.
+ noise_eigenvec nchan Eigenvectors of the noise covariance matrix. In terms of Section 6.2.3, INLINE_EQUATION.
+ data nchan x ntime The measured data. One row contains the data at one time point.
+ times ntime The time points in the above matrix in seconds
+ nave 1 Number of averages as listed in the data file.
+ meas_times ntime The time points in seconds.
+ =================== ================== =============================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+
+.. _BEHCBCGG:
+
+Converting raw data to Matlab format
+####################################
+
+The utility mne_raw2mat converts
+all or selected channels from a raw data file to a Matlab mat file.
+In addition, this utility can provide information about the raw
+data file so that the raw data can be read directly from the original
+fif file using Matlab file I/O routines.
+
+.. note:: The MNE Matlab toolbox described in Chapter 10 provides direct access to raw fif files without a need for conversion to mat file format first. Therefore, it is recommended that you use the Matlab toolbox rather than mne_raw2mat which creates large files occupying disk space unnecessarily.
+
+Command-line options
+====================
+
+mne_raw2mat accepts the
+following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---raw <name>**
+
+ Specifies the name of the raw data fif file to convert.
+
+**\---mat <name>**
+
+ Specifies the name of the destination Matlab file.
+
+**\---info**
+
+ With this option present, only information about the raw data file
+ is included. The raw data itself is omitted.
+
+**\---sel <name>**
+
+ Specifies a text file which contains the names of the channels to include
+ in the output file, one channel name per line. If the ``--info`` option
+ is specified, ``--sel`` does not have any effect.
+
+**\---tag <tag>**
+
+ By default, all Matlab variables included in the output file start
+ with MNE_. This option changes the prefix to <tag> _.
+
+Matlab data structures
+======================
+
+The Matlab files output by mne_raw2mat can
+contain two data structures, <tag>_raw and <tag>_raw_info .
+If ``--info`` option is specifed, the file contains the
+latter structure only.
+
+The <tag>_raw stucture
+contains only one field, data which
+is a matrix containing the raw data. Each row of this matrix constitutes
+the data from one channel in the original file. The data type of
+this matrix is the same of the original data (2-byte signed integer,
+4-byte signed integer, or single-precision float).
+
+The fields of the <tag>_raw_info structure
+are listed in :ref:`BEHFDCIH`. Further explanation of the bufs field
+is provided in :ref:`BEHJEIHJ`.
+
+.. _BEHFDCIH:
+
+.. table:: The fields of the raw data info structure.
+
+ ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+ Variable Size Description
+ ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+ orig_file string The name of the original fif file specified with the ``--raw`` option.
+ nchan 1 Number of channels.
+ nsamp 1 Total number of samples
+ bufs nbuf x 4 This field is present if ``--info`` option was specified on the command line. For details, see :ref:`BEHJEIHJ`.
+ sfreq 1 The sampling frequency in Hz.
+ lowpass 1 Lowpass filter frequency (Hz)
+ highpass 1 Highpass filter frequency (Hz)
+ ch_names nchan (string) String array containing the names of the channels included
+ ch_types nchan x 2 The column lists the types of the channesl (1 = MEG, 2 = EEG). The second column lists the coil types, see Tables 5.2 and 5.3. For EEG electrodes, this value equals one.
+ ch_lognos nchan x 1 Logical channel numbers as listed in the fiff file
+ ch_units nchan x 2 Units and unit multipliers as listed in the fif file. The unit of the data is listed in the first column (T = 112, T/m = 201, V = 107). At present, the second column will be always zero, *i.e.*, no unit multiplier.
+ ch_pos nchan x 12 The location information for each channel. The first three values specify the origin of the sensor coordinate system or the location of the electrode. For MEG channels, the following nine number specify the *x*, *y*, and *z*-direction unit vectors of the sensor coordinate system. For EEG electrodes the first vector after the electrode location specifies the location of the reference electrode. If the reference is not specified this value is all z [...]
+ ch_cals nchan x 2 The raw data output by mne_raw2mat is uncalibrated. The first column is the range member of the fiff data structures and while the second is the cal member. To get calibrared data values in the units given in ch_units from the raw data, the data must be multiplied with the product of range and cal .
+ meg_head_trans 4 x 4 The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates.
+ ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+
+.. _BEHJEIHJ:
+
+.. table:: The bufs member of the raw data info structure.
+
+ ======== ===========================================================================================================================================================================================================================
+ Column Contents
+ ======== ===========================================================================================================================================================================================================================
+ 1 The raw data type (2 or 16 = 2-byte signed integer, 3 = 4-byte signed integer, 4 = single-precision float). All data in the fif file are written in the big-endian byte order. The raw data are stored sample by sample.
+ 2 Byte location of this buffer in the original fif file.
+ 3 First sample of this buffer. Since raw data storing can be switched on and off during the acquisition, there might be gaps between the end of one buffer and the beginning of the next.
+ 4 Number of samples in the buffer.
+ ======== ===========================================================================================================================================================================================================================
+
+.. _BEHFIDCB:
+
+Converting epochs to Matlab format
+##################################
+
+The utility mne_epochs2mat converts
+epoch data including all or selected channels from a raw data file
+to a simple binary file with an associated description file in Matlab
+mat file format. With help of the description file, a matlab program
+can easily read the epoch data from the simple binary file. Signal
+space projection and bandpass filtering can be optionally applied
+to the raw data prior to saving the epochs.
+
+.. note:: The MNE Matlab toolbox described in Chapter 10 provides direct access to raw fif files without conversion with mne_epochs2mat first. Therefore, it is recommended that you use the Matlab toolbox rather than mne_epochs2mat which creates large files occupying disk space unnecessarily. An exception to this is the case where you apply a filter to the data and save the band-pass filtered epochs.
+
+Command-line options
+====================
+
+mne_epochs2mat accepts
+the following command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---raw <name>**
+
+ Specifies the name of the raw data fif file to use as input.
+
+**\---mat <name>**
+
+ Specifies the name of the destination file. Anything following the last
+ period in the file name will be removed before composing the output
+ file name. The binary epoch file will be called <trimmed name> ``.epochs`` and
+ the corresponding Matlab description file will be <trimmed name> ``_desc.mat`` .
+
+**\---tag <tag>**
+
+ By default, all Matlab variables included in the description file
+ start with MNE_. This option changes the prefix to <tag> _.
+
+**\---events <name>**
+
+ The file containing the event definitions. This can be a text or
+ fif format file produced by mne_process_raw or mne_browse_raw ,
+ see Section 4.10.5. With help of this file it is possible
+ to select virtually any data segment from the raw data file. If
+ this option is missing, the digital trigger channel in the raw data
+ file or a fif format event file produced automatically by mne_process_raw or mne_browse_raw is
+ consulted for event information.
+
+**\---event <name>**
+
+ Event number identifying the epochs of interest.
+
+**\---tmin <time/ms>**
+
+ The starting point of the epoch with respect to the event of interest.
+
+**\---tmax <time/ms>**
+
+ The endpoint of the epoch with respect to the event of interest.
+
+**\---sel <name>**
+
+ Specifies a text file which contains the names of the channels to include
+ in the output file, one channel name per line. If the ``--inv`` option
+ is specified, ``--sel`` is ignored. If neither ``--inv`` nor ``--sel`` is
+ present, all MEG and EEG channels are included. The digital trigger
+ channel can be included with the ``--includetrig`` option, described
+ below.
+
+**\---inv <name>**
+
+ Specifies an inverse operator, which will be employed in two ways. First,
+ the channels included to output will be those included in the inverse
+ operator. Second, any signal-space projection operator present in
+ the inverse operator file will be applied to the data. This option
+ cancels the effect of ``--sel`` and ``--proj`` options.
+
+**\---digtrig <name>**
+
+ Name of the composite digital trigger channel. The default value
+ is 'STI 014'. Underscores in the channel name
+ will be replaced by spaces.
+
+**\---digtrigmask <number>**
+
+ Mask to be applied to the trigger channel values before considering them.
+ This option is useful if one wants to set some bits in a don't care
+ state. For example, some finger response pads keep the trigger lines
+ high if not in use, *i.e.*, a finger is not in
+ place. Yet, it is convenient to keep these devices permanently connected
+ to the acquisition system. The number can be given in decimal or
+ hexadecimal format (beginning with 0x or 0X). For example, the value
+ 255 (0xFF) means that only the lowest order byte (usually trigger
+ lines 1 - 8 or bits 0 - 7) will be considered.
+
+**\---includetrig**
+
+ Add the digital trigger channel to the list of channels to output.
+ This option should not be used if the trigger channel is already
+ included in the selection specified with the ``--sel`` option.
+
+**\---filtersize <size>**
+
+ Adjust the length of the FFT to be applied in filtering. The number will
+ be rounded up to the next power of two. If the size is INLINE_EQUATION,
+ the corresponding length of time is INLINE_EQUATION,
+ where INLINE_EQUATION is the sampling frequency
+ of your data. The filtering procedure includes overlapping tapers
+ of length INLINE_EQUATION so that the total FFT
+ length will actually be INLINE_EQUATION. The default
+ value is 4096.
+
+**\---highpass <value/Hz>**
+
+ Highpass filter frequency limit. If this is too low with respect
+ to the selected FFT length and data file sampling frequency, the
+ data will not be highpass filtered. You can experiment with the
+ interactive version to find the lowest applicable filter for your
+ data. This value can be adjusted in the interactive version of the
+ program. The default is 0, i.e., no highpass filter in effect.
+
+**\---highpassw <value/Hz>**
+
+ The width of the transition band of the highpass filter. The default
+ is 6 frequency bins, where one bin is INLINE_EQUATION.
+
+**\---lowpass <value/Hz>**
+
+ Lowpass filter frequency limit. This value can be adjusted in the interactive
+ version of the program. The default is 40 Hz.
+
+**\---lowpassw <value/Hz>**
+
+ The width of the transition band of the lowpass filter. This value
+ can be adjusted in the interactive version of the program. The default
+ is 5 Hz.
+
+**\---filteroff**
+
+ Do not filter the data.
+
+**\---proj <name>**
+
+ Include signal-space projection (SSP) information from this file.
+ If the ``--inv`` option is present, ``--proj`` has
+ no effect.
+
+.. note:: Baseline has not been subtracted from the epochs. This has to be done in subsequent processing with Matlab if so desired.
+
+.. note:: Strictly speaking, trigger mask value zero would mean that all trigger inputs are ignored. However, for convenience, setting the mask to zero or not setting it at all has the same effect as 0xFFFFFFFF, *i.e.*, all bits set.
+
+.. note:: The digital trigger channel can also be set with the MNE_TRIGGER_CH_NAME environment variable. Underscores in the variable value will *not* be replaced with spaces by mne_browse_raw or mne_process_raw . Using the ``--digtrig`` option supersedes the MNE_TRIGGER_CH_NAME environment variable.
+
+.. note:: The digital trigger channel mask can also be set with the MNE_TRIGGER_CH_MASK environment variable. Using the ``--digtrigmask`` option supersedes the MNE_TRIGGER_CH_MASK environment variable.
+
+The binary epoch data file
+==========================
+
+mne_epochs2mat saves the
+epoch data extracted from the raw data file is a simple binary file.
+The data are stored as big-endian single-precision floating point
+numbers. Assuming that each of the total of INLINE_EQUATION epochs
+contains INLINE_EQUATION channels and INLINE_EQUATION time
+points, the data INLINE_EQUATION ar e ordered
+as
+
+.. math:: 1 + 1 = 2
+
+where the first index stands for the time point, the second
+for the channel, and the third for the epoch number, respectively.
+The data are not calibrated, i.e., the calibration factors present
+in the Matlab description file have to be applied to get to physical
+units as described below.
+
+.. note:: The maximum size of an epoch data file is 2 Gbytes, *i.e.*, 0.5 Gsamples.
+
+Matlab data structures
+======================
+
+The Matlab description files output by mne_epochs2mat contain
+a data structure <tag>_epoch_info .
+The fields of the this structure are listed in :ref:`BEHFDCIH`.
+Further explanation of the epochs member
+is provided in :ref:`BEHHAGHE`.
+
+.. _BEHIFJIJ:
+
+.. table:: The fields of the raw data info structure.
+
+ ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+ Variable Size Description
+ ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+ orig_file string The name of the original fif file specified with the ``--raw`` option.
+ epoch_file string The name of the epoch data file produced by mne_epocs2mat .
+ nchan 1 Number of channels.
+ nepoch 1 Total number of epochs.
+ epochs nepoch x 5 Description of the content of the epoch data file, see :ref:`BEHHAGHE`.
+ sfreq 1 The sampling frequency in Hz.
+ lowpass 1 Lowpass filter frequency (Hz)
+ highpass 1 Highpass filter frequency (Hz)
+ ch_names nchan (string) String array containing the names of the channels included
+ ch_types nchan x 2 The column lists the types of the channels (1 = MEG, 2 = EEG). The second column lists the coil types, see Tables 5.2 and 5.3. For EEG electrodes, this value equals one.
+ ch_lognos nchan x 1 Logical channel numbers as listed in the fiff file
+ ch_units nchan x 2 Units and unit multipliers as listed in the fif file. The unit of the data is listed in the first column (T = 112, T/m = 201, V = 107). At present, the second column will be always zero, *i.e.*, no unit multiplier.
+ ch_pos nchan x 12 The location information for each channel. The first three values specify the origin of the sensor coordinate system or the location of the electrode. For MEG channels, the following nine number specify the *x*, *y*, and *z*-direction unit vectors of the sensor coordinate system. For EEG electrodes the first vector after the electrode location specifies the location of the reference electrode. If the reference is not specified this value is all z [...]
+ ch_cals nchan x 2 The raw data output by mne_raw2mat are not calibrated. The first column is the range member of the fiff data structures and while the second is the cal member. To get calibrated data values in the units given in ch_units from the raw data, the data must be multiplied with the product of range and cal .
+ meg_head_trans 4 x 4 The coordinate frame transformation from the MEG device coordinates to the MEG head coordinates.
+ ================= ================= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================== [...]
+
+.. _BEHHAGHE:
+
+.. table:: The epochs member of the raw data info structure.
+
+ ======== ================================================================================================================================================================================================================
+ Column Contents
+ ======== ================================================================================================================================================================================================================
+ 1 The raw data type (2 or 16 = 2-byte signed integer, 3 = 4-byte signed integer, 4 = single-precision float). The epoch data are written using the big-endian byte order. The data are stored sample by sample.
+ 2 Byte location of this epoch in the binary epoch file.
+ 3 First sample of this epoch in the original raw data file.
+ 4 First sample of the epoch with respect to the event.
+ 5 Number of samples in the epoch.
+ ======== ================================================================================================================================================================================================================
+
+.. note:: For source modelling purposes, it is recommended that the MNE Matlab toolbox, see Chapter 10 is employed to read the measurement info instead of using the channel information in the raw data info structure described in :ref:`BEHIFJIJ`.
diff --git a/doc/source/manual/cookbook.rst b/doc/source/manual/cookbook.rst
new file mode 100644
index 0000000..5255e27
--- /dev/null
+++ b/doc/source/manual/cookbook.rst
@@ -0,0 +1,1058 @@
+
+
+.. _CHDDJDAA:
+
+============
+The Cookbook
+============
+
+Overview
+########
+
+This section describes the typical workflow needed to produce
+the minimum-norm estimate movies using the MNE software. The workflow
+is summarized in :ref:`CIHBIIAH`.
+
+.. _CIHBIIAH:
+
+.. figure:: picture.png
+ :alt: none
+
+ Workflow of the MNE software. References in parenthesis indicate sections and chapters of this manual.
+
+Selecting the subject
+#####################
+
+Before starting the data analysis, setup the environment
+variable SUBJECTS_DIR to select the directory under which the anatomical
+MRI data are stored. Optionally, set SUBJECT as the name of the
+subject's MRI data directory under SUBJECTS_DIR. With this
+setting you can avoid entering the --subject option common to many
+MNE programs and scripts. In the following sections, files in the
+FreeSurfer directory hierarchy are usually referred to without specifying
+the leading directories. Thus, bem/msh-7-src.fif is used to refer
+to the file $SUBJECTS_DIR/$SUBJECT/bem/msh-7-src.fif.
+
+It is also recommended that the FreeSurfer environment
+is set up before using the MNE software.
+
+.. _CHDBBCEJ:
+
+Cortical surface reconstruction with FreeSurfer
+###############################################
+
+The first processing stage is the creation of various surface
+reconstructions with FreeSurfer .
+The recommended FreeSurfer workflow
+is summarized on the FreeSurfer wiki pages: https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction.
+Please refer to the FreeSurfer wiki pages
+(https://surfer.nmr.mgh.harvard.edu/fswiki/) and other FreeSurfer documentation
+for more information.
+
+.. note:: Only the latest (4.0.X and later) FreeSurfer distributions contain a version of tkmedit which is compatible with mne_analyze , see Section 7.18.
+
+.. _BABCCEHF:
+
+Setting up the anatomical MR images for MRIlab
+##############################################
+
+If you have the Neuromag software installed, the Neuromag
+MRI viewer, MRIlab, can be used to access the MRI slice data created
+by FreeSurfer . In addition, the
+Neuromag MRI directories can be used for storing the MEG/MRI coordinate
+transformations created with mne_analyze ,
+see Section 7.16. Doring the computation of the forward
+solution, mne_do_forwand_solution searches
+for the MEG/MRI coordinate in the Neuromag MRI directories, see :ref:`BABCHEJD`. The fif files created by mne_setup_mrit can
+be loaded into Matlab with the fiff_read_mri function,
+see Chapter 10.
+
+These functions require running the script mne_setup_mri which
+requires that the subject is set with the ``--subject`` option
+or by the SUBJECT environment variable. The script processes one
+or more MRI data sets from ``$SUBJECTS_DIR/$SUBJECT/mri`` ,
+by default they are T1 and brain. This default can be changed by
+specifying the sets by one or more ``--mri`` options.
+
+The script creates the directories ``mri/`` <name> ``-neuromag/slices`` and ``mri/`` <name> ``-neuromag/sets`` .
+If the the input data set is in COR format, mne_setup_mri makes
+symbolic links from the COR files in the directory ``mri/`` <name> into ``mri/`` <name> ``-neuromag/slices`` ,
+and creates a corresponding fif file COR.fif in ``mri/`` <name> ``-neuromag/sets`` ..
+This "description file" contains references to
+the actual MRI slices.
+
+If the input MRI data are stored in the newer mgz format,
+the file created in the ``mri/`` <name> ``-neuromag/sets`` directory
+will include the MRI pixel data as well. If available, the coordinate
+transformations to allow conversion between the MRI (surface RAS)
+coordinates and MNI and FreeSurfer Talairach coordinates are copied
+to the MRI description file. mne_setup_mri invokes mne_make_cor_set ,
+described in Section 9.8 to convert the data.
+
+For example:
+
+``mne_setup_mri --subject duck_donald --mri T1``
+
+This command processes the MRI data set T1 for subject duck_donald.
+
+.. note:: If the SUBJECT environment variable is set it is usually sufficient to run mne_setup_mri without any options.
+
+.. note:: If the name specified with the ``--mri`` option contains a slash, the MRI data are accessed from the directory specified and the ``SUBJECT`` and ``SUBJECTS_DIR`` environment variables as well as the ``--subject`` option are ignored.
+
+.. _CIHCHDAE:
+
+Setting up the source space
+###########################
+
+This stage consists of the following:
+
+- Creating a suitable decimated dipole
+ grid on the white matter surface.
+
+- Creating the source space file in fif format.
+
+- Creating ascii versions of the source space file for viewing
+ with MRIlab.
+
+All of the above is accomplished with the convenience script mne_setup_source_space . This
+script assumes that:
+
+- The anatomical MRI processing has been
+ completed as described in :ref:`CHDBBCEJ`.
+
+- The environment variable SUBJECTS_DIR is set correctly.
+
+The script accepts the following options:
+
+**\---subject <subject>**
+
+ Defines the name of the subject. If the environment variable SUBJECT
+ is set correctly, this option is not required.
+
+**\---morph <name>**
+
+ Name of a subject in SUBJECTS_DIR. If this option is present, the source
+ space will be first constructed for the subject defined by the --subject
+ option or the SUBJECT environment variable and then morphed to this
+ subject. This option is useful if you want to create a source spaces
+ for several subjects and want to directly compare the data across
+ subjects at the source space vertices without any morphing procedure
+ afterwards. The drawback of this approach is that the spacing between
+ source locations in the "morph" subject is not going
+ to be as uniform as it would be without morphing.
+
+**\---spacing <spacing/mm>**
+
+ Specifies the grid spacing for the source space in mm. If not set,
+ a default spacing of 7 mm is used. Either the default or a 5-mm
+ spacing is recommended.
+
+**\---ico <number>**
+
+ Instead of using the traditional method for cortical surface decimation
+ it is possible to create the source space using the topology of
+ a recursively subdivided icosahedron (<number> > 0)
+ or an octahedron (<number> < 0).
+ This method uses the cortical surface inflated to a sphere as a
+ tool to find the appropriate vertices for the source space. The
+ benefit of the ``--ico`` option is that the source space
+ will have triangulation information for the decimated vertices included, which
+ future versions of MNE software may be able to utilize. The number
+ of triangles increases by a factor of four in each subdivision,
+ starting from 20 triangles in an icosahedron and 8 triangles in an
+ octahedron. Since the number of vertices on a closed surface is INLINE_EQUATION,
+ the number of vertices in the *k*th subdivision of
+ an icosahedron and an octahedron are INLINE_EQUATION and INLINE_EQUATION, respectively.
+ The recommended values for <number> and
+ the corresponding number of source space locations are listed in :ref:`BABGCDHA`.
+
+**\---surface <name>**
+
+ Name of the surface under the surf directory to be used. Defaults
+ to 'white'. ``mne_setup_source_space`` looks
+ for files ``rh.`` <name> and ``lh.`` <name> under
+ the ``surf`` directory.
+
+**\---overwrite**
+
+ An existing source space file with the same name is overwritten only
+ if this option is specified.
+
+**\---cps**
+
+ Compute the cortical patch statistics. This is need if current-density estimates
+ are computed, see Section 6.2.8. If the patch information is
+ available in the source space file the surface normal is considered to
+ be the average normal calculated over the patch instead of the normal
+ at each source space location. The calculation of this information
+ takes a considerable amount of time because of the large number
+ of Dijkstra searches involved.
+
+.. _BABGCDHA:
+
+.. table:: Recommended subdivisions of an icosahedron and an octahedron for the creation of source spaces. The approximate source spacing and corresponding surface area have been calculated assuming a 1000-cm2 surface area per hemisphere.
+
+ ========== ======================== ===================== ===============================
+ <number> Sources per hemisphere Source spacing / mm Surface area per source / mm2
+ ========== ======================== ===================== ===============================
+ -5 1026 9.9 97
+ 4 2562 6.2 39
+ -6 4098 4.9 24
+ 5 10242 3.1 9.8
+ ========== ======================== ===================== ===============================
+
+For example, to create the reconstruction geometry for Donald
+Duck with a 5-mm spacing between the grid points, say
+
+``mne_setup_source_space --subject duck_donald --spacing 5``
+
+As a result, the following files are created into the ``bem`` directory:
+
+- <subject>-<spacing>- ``src.fif`` containing
+ the source space description in fif format.
+
+- <subject>-<spacing>- ``lh.pnt`` and <subject>-<spacing>- ``rh.pnt`` containing
+ the source space points in MRIlab compatible ascii format.
+
+- <subject>-<spacing>- ``lh.dip`` and <subject>-<spacing>- ``rh.dip`` containing
+ the source space points in MRIlab compatible ascii format. These
+ files contain 'dipoles', *i.e.*,
+ both source space points and cortex normal directions.
+
+- If cortical patch statistics is requested, another source
+ space file called <subject>-<spacing> ``p-src.fif`` will
+ be created.
+
+.. note:: <spacing> will be the suggested source spacing in millimeters if the ``--spacing`` option is used. For source spaces based on *k*th subdivision of an icosahedron, <spacing> will be replaced by ``ico-`` k or ``oct-`` k , respectively.
+
+.. note:: After the geometry is set up it is possible to check that the source space points are located on the cortical surface. This can be easily done with by loading the ``COR.fif`` file from ``mri/T1/neuromag/sets`` into MRIlab and by subsequently overlaying the corresponding pnt or dip files using Import/Strings or Import/Dipoles from the File menu, respectively.
+
+.. note:: If the SUBJECT environment variable is set correctly it is usually sufficient to run ``mne_setup_source_space`` without any options.
+
+.. _CHDBJCIA:
+
+Creating the BEM model meshes
+#############################
+
+Calculation of the forward solution using the boundary-element
+model (BEM) requires that the surfaces separating regions of different
+electrical conductivities are tessellated with suitable surface
+elements. Our BEM software employs triangular tessellations. Therefore,
+prerequisites for BEM calculations are the segmentation of the MRI
+data and the triangulation of the relevant surfaces.
+
+For MEG computations, a reasonably accurate solution can
+be obtained by using a single-compartment BEM assuming the shape
+of the intracranial volume. For EEG, the standard model contains
+the intracranial space, the skull, and the scalp.
+
+At present, no bulletproof method exists for creating the
+triangulations. Feasible approaches are described in Appendix A.
+
+.. _BABDBBFC:
+
+Setting up the triangulation files
+==================================
+
+The segmentation algorithms described in Appendix A produce
+either FreeSurfer surfaces or triangulation
+data in text. Before proceeding to the creation of the boundary
+element model, standard files (or symbolic links created with the ``ln -s`` command) have to be present in the subject's ``bem`` directory.
+If you are employing ASCII triangle files the standard file names
+are:
+
+**inner_skull.tri**
+
+ Contains the inner skull triangulation.
+
+**outer_skull.tri**
+
+ Contains the outer skull triangulation.
+
+**outer_skin.tri**
+
+ Contains the head surface triangulation.
+
+The corresponding names for FreeSurfer surfaces
+are:
+
+**inner_skull.surf**
+
+ Contains the inner skull triangulation.
+
+**outer_skull.surf**
+
+ Contains the outer skull triangulation.
+
+**outer_skin.surf**
+
+ Contains the head surface triangulation.
+
+.. note:: Different methods can be employed for the creation of the individual surfaces. For example, it may turn out that the watershed algorithm produces are better quality skin surface than the segmentation approach based on the FLASH images. If this is the case, ``outer_skin.surf`` can set to point to the corresponding watershed output file while the other surfaces can be picked from the FLASH segmentation data.
+
+.. note:: The triangulation files can include name of the subject as a prefix ``<subject name>-`` , *e.g.*, ``duck-inner_skull.surf`` .
+
+.. note:: The mne_convert_surface utility described in Section 9.7 can be used to convert text format triangulation files into the FreeSurfer surface format.
+
+.. note:: "Aliases" created with the Mac OSX finder are not equivalent to symbolic links and do not work as such for the UNIX shells and MNE programs.
+
+.. _CIHDBFEG:
+
+Setting up the boundary-element model
+#####################################
+
+This stage sets up the subject-dependent data for computing
+the forward solutions:
+
+- The fif format boundary-element model
+ geometry file is created. This step also checks that the input surfaces
+ are complete and that they are topologically correct, *i.e.*,
+ that the surfaces do not intersect and that the surfaces are correctly
+ ordered (outer skull surface inside the scalp and inner skull surface
+ inside the outer skull). Furthermore, the range of triangle sizes
+ on each surface is reported. For the three-layer model, the minimum
+ distance between the surfaces is also computed.
+
+- Text files containing the boundary surface vertex coordinates are
+ created.
+
+- The the geometry-dependent BEM solution data are computed. This step
+ can be optionally omitted. This step takes several minutes to complete.
+
+This step assigns the conductivity values to the BEM compartments.
+For the scalp and the brain compartments, the default is 0.3 S/m.
+The defalt skull conductivity is 50 times smaller, *i.e.*,
+0.006 S/m. Recent publications, see Section 13.3, report
+a range of skull conductivity ratios ranging from 1:15 (Oostendorp *et
+al.*, 2000) to 1:25 - 1:50 (Slew *et al.*,
+2009, Conçalves *et al.*, 2003). The
+MNE default ratio 1:50 is based on the typical values reported in
+(Conçalves *et al.*, 2003), since their
+approach is based comparison of SEF/SEP measurements in a BEM model.
+The variability across publications may depend on individual variations
+but, more importantly, on the precision of the skull compartment
+segmentation.
+
+This processing stage is automated with the script mne_setup_forward_model . This
+script assumes that:
+
+- The anatomical MRI processing has been
+ completed as described in :ref:`CHDBBCEJ`.
+
+- The BEM model meshes have been created as outlined in :ref:`CHDBJCIA`.
+
+- The environment variable SUBJECTS_DIR is set correctly.
+
+mne_setup_forward_model accepts
+the following options:
+
+**\---subject <subject>**
+
+ Defines the name of the subject. This can be also accomplished
+ by setting the SUBJECT environment variable.
+
+**\---surf**
+
+ Use the FreeSurfer surface files instead of the default ASCII triangulation
+ files. Please consult :ref:`BABDBBFC` for the standard file
+ naming scheme.
+
+**\---noswap**
+
+ Traditionally, the vertices of the triangles in 'tri' files
+ have been ordered so that, seen from the outside of the triangulation,
+ the vertices are ordered in clockwise fashion. The fif files, however,
+ employ the more standard convention with the vertices ordered counterclockwise.
+ Therefore, mne_setup_forward_model by
+ default reverses the vertex ordering before writing the fif file.
+ If, for some reason, you have counterclockwise-ordered tri files
+ available this behavior can be turned off by defining ``--noswap`` .
+ When the fif file is created, the vertex ordering is checked and
+ the process is aborted if it is incorrect after taking into account
+ the state of the swapping. Should this happen, try to run mne_setup_forward_model again including
+ the ``--noswap`` flag. In particular, if you employ the seglab software
+ to create the triangulations (see Appendix A), the ``--noswap`` flag
+ is required. This option is ignored if ``--surf`` is specified
+
+**\---ico <number>**
+
+ This option is relevant (and required) only with the ``--surf`` option and
+ if the surface files have been produced by the watershed algorithm.
+ The watershed triangulations are isomorphic with an icosahedron,
+ which has been recursively subdivided six times to yield 20480 triangles.
+ However, this number of triangles results in a long computation
+ time even in a workstation with generous amounts of memory. Therefore,
+ the triangulations have to be decimated. Specifying ``--ico 4`` yields 5120 triangles per surface while ``--ico 3`` results
+ in 1280 triangles. The recommended choice is ``--ico 4`` .
+
+**\---homog**
+
+ Use a single compartment model (brain only) instead a three layer one
+ (scalp, skull, and brain). Only the ``inner_skull.tri`` triangulation
+ is required. This model is usually sufficient for MEG but invalid
+ for EEG. If you are employing MEG data only, this option is recommended
+ because of faster computation times. If this flag is specified,
+ the options ``--brainc`` , ``--skullc`` , and ``--scalpc`` are irrelevant.
+
+**\---brainc <conductivity/ S/m>**
+
+ Defines the brain compartment conductivity. The default value is 0.3 S/m.
+
+**\---skullc <conductivity/ S/m>**
+
+ Defines the skull compartment conductivity. The default value is 0.006 S/m
+ corresponding to a conductivity ratio 1/50 between the brain and
+ skull compartments.
+
+**\---scalpc <conductivity/ S/m>**
+
+ Defines the brain compartment conductivity. The default value is 0.3 S/m.
+
+**\---innershift <value/mm>**
+
+ Shift the inner skull surface outwards along the vertex normal directions
+ by this amount.
+
+**\---outershift <value/mm>**
+
+ Shift the outer skull surface outwards along the vertex normal directions
+ by this amount.
+
+**\---scalpshift <value/mm>**
+
+ Shift the scalp surface outwards along the vertex normal directions by
+ this amount.
+
+**\---nosol**
+
+ Omit the BEM model geometry dependent data preparation step. This
+ can be done later by running mne_setup_forward_model without the ``--nosol`` option.
+
+**\---model <name>**
+
+ Name for the BEM model geometry file. The model will be created into
+ the directory bem as <name>- ``bem.fif`` . If
+ this option is missing, standard model names will be used (see below).
+
+As a result of running the mne_setup_foward_model script, the
+following files are created into the ``bem`` directory:
+
+- BEM model geometry specifications <subject>-<ntri-scalp>-<ntri-outer_skull>-<ntri-inner_skull>- ``bem.fif`` or <subject>-<ntri-inner_skull> ``-bem.fif`` containing
+ the BEM geometry in fif format. The latter file is created if -homog
+ option is specified. Here, <ntri-xxx> indicates
+ the number of triangles on the corresponding surface.
+
+- <subject>-<surface name>-<ntri> ``.pnt`` files
+ are created for each of the surfaces present in the BEM model. These
+ can be loaded to MRIlab to check the location of the surfaces.
+
+- <subject>-<surface name>-<ntri> ``.surf`` files
+ are created for each of the surfaces present in the BEM model. These
+ can be loaded to tkmedit to check
+ the location of the surfaces.
+
+- The BEM 'solution' file containing the geometry
+ dependent solution data will be produced with the same name as the
+ BEM geometry specifications with the ending ``-bem-sol.fif`` .
+ These files also contain all the information in the ``-bem.fif`` files.
+
+After the BEM is set up it is advisable to check that the
+BEM model meshes are correctly positioned. This can be easily done
+with by loading the COR.fif file
+from mri/T1-neuromag/sets into
+MRIlab and by subsequently overlaying the corresponding pnt files
+using Import/Strings from the File menu.
+
+.. note:: The FreeSurfer format BEM surfaces can be also viewed with the tkmedit program which is part of the FreeSurfer distribution.
+
+.. note:: If the SUBJECT environment variable is set, it is usually sufficient to run ``mne_setup_forward_model`` without any options for the three-layer model and with the ``--homog`` option for the single-layer model. If the input files are FreeSurfer surfaces, ``--surf`` and ``--ico 4`` are required as well.
+
+.. note:: With help of the ``--nosol`` option it is possible to create candidate BEM geometry data files quickly and do the checking with respect to the anatomical MRI data. When the result is satisfactory, mne_setup_forward_model can be run without ``--nosol`` to invoke the time-consuming calculation of the solution file as well.
+
+.. note:: The triangle meshes created by the seglab program have counterclockwise vertex ordering and thus require the --noswap option.
+
+.. note:: Up to this point all processing stages depend on the anatomical (geometrical) information only and thus remain identical across different MEG studies.
+
+Setting up the MEG/EEG analysis directory
+#########################################
+
+The remaining steps require that the actual MEG/EEG data
+are available. It is recommended that a new directory is created
+for the MEG/EEG data processing. The raw data files collected should not be
+copied there but rather referred to with symbolic links created
+with the ``ln -s`` command. Averages calculated
+on-line can be either copied or referred to with links.
+
+.. note:: If you don't know how to create a directory, how to make symbolic links, or how to copy files from the shell command line, this is a perfect time to learn about this basic skills from other users or from a suitable elementary book before proceeding.
+
+Preprocessing the raw data
+##########################
+
+The following MEG and EEG data preprocessing steps are recommended:
+
+- The coding problems on the trigger channel
+ STI 014 may have to fixed, see :ref:`BABCDBDI`.
+
+- EEG electrode location information and MEG coil types may
+ need to be fixed, see :ref:`BABCDFJH`.
+
+- The data may be optionally downsampled to facilitate subsequent
+ processing, see :ref:`BABDGFFG`.
+
+- Bad channels in the MEG and EEG data must be identified, see :ref:`BABBHCFG`
+
+- The data has to be filtered to the desired passband. If mne_browse_raw or mne_process_raw is
+ employed to calculate the offline averages and covariance matrices,
+ this step is unnecessary since the data are filtered on the fly.
+ For information on these programs, please consult Chapter 4.
+
+- For evoked-response analysis, the data has to be re-averaged
+ off line, see :ref:`BABEAEDF`.
+
+.. _BABCDBDI:
+
+Cleaning the digital trigger channel
+====================================
+
+The calibration factor of the digital trigger channel used
+to be set to a value much smaller than one by the Neuromag data
+acquisition software. Especially to facilitate viewing of raw data
+in graph it is advisable to change the calibration factor to one.
+Furthermore, the eighth bit of the trigger word is coded incorrectly
+in the original raw files. Both problems can be corrected by saying:
+
+``mne_fix_stim14`` <raw file>
+
+More information about mne_fix_stim14 is
+available in Section 11.4.2. It is recommended that this
+fix is included as the first raw data processing step. Note, however,
+the mne_browse_raw and mne_process_raw always sets
+the calibration factor to one internally.
+
+.. note:: If your data file was acquired on or after November 10, 2005 on the Martinos center Vectorview system, it is not necessary to use mne_fix_stim14 .
+
+.. _BABCDFJH:
+
+Fixing channel information
+==========================
+
+There are two potential discrepancies in the channel information
+which need to be fixed before proceeding:
+
+- EEG electrode locations may be incorrect
+ if more than 60 EEG channels are acquired.
+
+- The magnetometer coil identifiers are not always correct.
+
+These potential problems can be fixed with the utilities mne_check_eeg_locations and mne_fix_mag_coil_types ,
+see Sections 11.4.3 and 11.4.4.
+
+.. _BABBHCFG:
+
+Designating bad channels
+========================
+
+Sometimes some MEG or EEG channels are not functioning properly
+for various reasons. These channels should be excluded from the
+analysis by marking them bad using the mne_mark_bad_channels utility,
+see Section 11.4.1. Especially if a channel is not show
+a signal at all (flat) it is most important to exclude it from the
+analysis, since its noise estimate will be unrealistically low and
+thus the current estimate calculations will give a strong weight
+to the zero signal on the flat channels and will essentially vanish.
+It is also important to exclude noisy channels because they can
+possibly affect others when signal-space projections or EEG average electrode
+reference is employed. Noisy bad channels can also adversely affect
+off-line averaging and noise-covariance matrix estimation by causing
+unnecessary rejections of epochs.
+
+Recommended ways to identify bad channels are:
+
+- Observe the quality of data during data
+ acquisition and make notes of observed malfunctioning channels to
+ your measurement protocol sheet.
+
+- View the on-line averages and check the condition of the channels.
+
+- Compute preliminary off-line averages with artefact rejection,
+ signal-space projection, and EEG average electrode reference computation
+ off and check the condition of the channels.
+
+- View raw data in mne_process_raw or
+ the Neuromag signal processor graph without
+ signal-space projection or EEG average electrode reference computation
+ and identify bad channels.
+
+.. note:: It is strongly recommended that bad channels are identified and marked in the original raw data files. If present in the raw data files, the bad channel selections will be automatically transferred to averaged files, noise-covariance matrices, forward solution files, and inverse operator decompositions.
+
+.. _BABDGFFG:
+
+Downsampling the MEG/EEG data
+=============================
+
+The minimum practical sampling frequency of the Vectorview
+system is 600 Hz. Lower sampling frequencies are allowed but result
+in elevated noise level in the data. It is advisable to lowpass
+filter and downsample the large raw data files often emerging in
+cognitive and patient studies to speed up subsequent processing.
+This can be accomplished with the mne_process_raw and mne_browse_raw software
+modules. For details, see Sections 4.2.3 and 4.4.3.
+
+.. note:: It is recommended that the original raw file is called <name>_raw.fif and the downsampled version <name>_ds_raw.fif , respectively.
+
+.. _BABEAEDF:
+
+Off-line averaging
+==================
+
+The recommended tools for off-line averaging are mne_browse_raw and mne_process_raw . mne_browse_raw is
+an interactive program for averaging and noise-covariance matrix
+computation. It also includes routines for filtering so that the
+downsampling and filtering steps can be skipped. Therefore, with mne_browse_raw you
+can produce the off-line average and noise-covariance matrix estimates
+directly. The batch-mode version of mne_brawse_raw is
+called mne_process_raw . Detailed
+information on mne_browse_raw and mne_process_raw can
+be found in Chapter 4.
+
+.. _CHDBEHDC:
+
+Aligning the coordinate frames
+##############################
+
+The calculation of the forward solution requires knowledge
+of the relative location and orientation of the MEG/EEG and MRI
+coordinate systems. The MEG/EEG head coordinate system is defined
+in Section 5.3. The conversion tools included in the MNE
+software take care of the idiosyncrasies of the coordinate frame
+definitions in different MEG and EEG systems so that the fif files
+always employ the same definition of the head coordinate system.
+
+Ideally, the head coordinate frame has a fixed orientation
+and origin with respect to the head anatomy. Therefore, a single
+MRI-head coordinate transformation for each subject should be sufficient.
+However, as explained in Section 5.3, the head coordinate
+frame is defined by identifying the fiducial landmark locations,
+making the origin and orientation of the head coordinate system
+slightly user dependent. As a result, the most conservative choice
+for the definition of the coordinate transformation computation
+is to re-establish it for each experimental session, *i.e.*,
+each time when new head digitization data are employed.
+
+The interactive source analysis software mne_analyze provides
+tools for coordinate frame alignment, see Chapter 7. Section 12.11 also
+contains tips for using mne_analyze for
+this purpose.
+
+Another useful tool for the coordinate system alignment is MRIlab ,
+the Neuromag MEG-MRI integration tool. Section 3.3.1 of the MRIlab User's
+Guide, Neuromag P/N NM20419A-A contains a detailed description of
+this task. Employ the images in the set ``mri/T1-neuromag/sets/COR.fif`` for
+the alignment. Check the alignment carefully using the digitization
+data included in the measurement file as described in Section 5.3.1
+of the above manual. Save the aligned description file in the same
+directory as the original description file without the alignment
+information but under a different name.
+
+.. warning:: This step is extremely important. If the alignment of the coordinate frames is inaccurate all subsequent processing steps suffer from the error. Therefore, this step should be performed by the person in charge of the study or by a trained technician. Written or photographic documentation of the alignment points employed during the MEG/EEG acquisition can also be helpful.
+
+.. _BABCHEJD:
+
+Computing the forward solution
+##############################
+
+After the MRI-MEG/EEG alignment has been set, the forward
+solution, *i.e.*, the magnetic fields and electric
+potentials at the measurement sensors and electrodes due to dipole
+sources located on the cortex, can be calculated with help of the
+convenience script mne_do_forward_solution .
+This utility accepts the following options:
+
+**\---subject <subject>**
+
+ Defines the name of the subject. This can be also accomplished
+ by setting the SUBJECT environment variable.
+
+**\---src <name>**
+
+ Source space name to use. This option overrides the ``--spacing`` option. The
+ source space is searched first from the current working directory
+ and then from ``$SUBJECTS_DIR/`` <subject> /bem.
+ The source space file must be specified exactly, including the ``fif`` extension.
+
+**\---spacing <spacing/mm> or ``ico-`` <number or ``oct-`` <number>**
+
+ This is an alternate way to specify the name of the source space
+ file. For example, if ``--spacing 6`` is given on the command
+ line, the source space files searched for are./<subject> -6-src.fif
+ and ``$SUBJECTS_DIR/$SUBJECT/`` bem/<subject> -6-src.fif.
+ The first file found is used. Spacing defaults to 7 mm.
+
+**\---bem <name>**
+
+ Specifies the BEM to be used. The name of the file can be any of <name> , <name> -bem.fif, <name> -bem-sol.fif.
+ The file is searched for from the current working directory and
+ from ``bem`` . If this option is omitted, the most recent
+ BEM file in the ``bem`` directory is used.
+
+**\---mri <name>**
+
+ The name of the MRI description file containing the MEG/MRI coordinate
+ transformation. This file was saved as part of the alignment procedure
+ outlined in :ref:`CHDBEHDC`. The file is searched for from
+ the current working directory and from ``mri/T1-neuromag/sets`` .
+ The search order for MEG/MRI coordinate transformations is discussed
+ below.
+
+**\---trans <name>**
+
+ The name of a text file containing the 4 x 4 matrix for the coordinate transformation
+ from head to mri coordinates, see below. If the option ``--trans`` is
+ present, the ``--mri`` option is not required. The search
+ order for MEG/MRI coordinate transformations is discussed below.
+
+**\---meas <name>**
+
+ This file is the measurement fif file or an off-line average file
+ produced thereof. It is recommended that the average file is employed for
+ evoked-response data and the original raw data file otherwise. This
+ file provides the MEG sensor locations and orientations as well as
+ EEG electrode locations as well as the coordinate transformation between
+ the MEG device coordinates and MEG head-based coordinates.
+
+**\---fwd <name>**
+
+ This file will contain the forward solution as well as the coordinate transformations,
+ sensor and electrode location information, and the source space
+ data. A name of the form <name> ``-fwd.fif`` is
+ recommended. If this option is omitted the forward solution file
+ name is automatically created from the measurement file name and
+ the source space name.
+
+**\---destdir <directory>**
+
+ Optionally specifies a directory where the forward solution will
+ be stored.
+
+**\---mindist <dist/mm>**
+
+ Omit source space points closer than this value to the inner skull surface.
+ Any source space points outside the inner skull surface are automatically
+ omitted. The use of this option ensures that numerical inaccuracies
+ for very superficial sources do not cause unexpected effects in
+ the final current estimates. Suitable value for this parameter is
+ of the order of the size of the triangles on the inner skull surface.
+ If you employ the seglab software
+ to create the triangulations, this value should be about equal to
+ the wish for the side length of the triangles.
+
+**\---megonly**
+
+ Omit EEG forward calculations.
+
+**\---eegonly**
+
+ Omit MEG forward calculations.
+
+**\---all**
+
+ Compute the forward solution for all vertices on the source space.
+
+**\---overwrite**
+
+ Overwrite the possibly existing forward model file.
+
+**\---help**
+
+ Show usage information for the script.
+
+The MEG/MRI transformation is determined by the following
+search sequence:
+
+- If the ``--mri`` option was
+ present, the file is looked for literally as specified, in the directory
+ of the measurement file specified with the ``--meas`` option,
+ and in the directory $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets.
+ If the file is not found, the script exits with an error message.
+
+- If the ``--trans`` option was present, the file is
+ looked up literally as specified. If the file is not found, the
+ script exists with an error message.
+
+- If neither ``--mri`` nor ``--trans`` option
+ was not present, the following default search sequence is engaged:
+
+ - The ``.fif`` ending in the
+ measurement file name is replaced by ``-trans.fif`` . If
+ this file is present, it will be used.
+
+ - The newest file whose name ends with ``-trans.fif`` in
+ the directory of the measurement file is looked up. If such a file
+ is present, it will be used.
+
+ - The newest file whose name starts with ``COR-`` in
+ directory $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets is looked
+ up. If such a file is present, it will be used.
+
+ - If all the above searches fail, the script exits with an error
+ message.
+
+This search sequence is designed to work well with the MEG/MRI
+transformation files output by mne_analyze ,
+see Section 7.16. It is recommended that -trans.fif file
+saved with the Save default and Save... options in
+the mne_analyze alignment dialog
+are used because then the $SUBJECTS_DIR/$SUBJECT directory will
+be composed of files which are dependent on the subjects's
+anatomy only, not on the MEG/EEG data to be analyzed.
+
+.. note:: If the standard MRI description file and BEM file selections are appropriate and the 7-mm source space grid spacing is appropriate, only the ``--meas`` option is necessary. If EEG data is not used ``--megonly`` option should be included.
+
+.. note:: If it is conceivable that the current-density transformation will be incorporated into the inverse operator, specify a source space with patch information for the forward computation. This is not mandatory but saves a lot of time when the inverse operator is created, since the patch information does not need to be created at that stage.
+
+.. note:: The MEG head to MRI transformation matrix specified with the ``--trans`` option should be a text file containing a 4-by-4 matrix:
+
+.. math:: 1 + 1 = 2
+
+defined so that if the augmented location vectors in MRI
+head and MRI coordinate systems are denoted by INLINE_EQUATION and INLINE_EQUATION,
+respectively,
+
+.. math:: 1 + 1 = 2
+
+.. note:: It is not possible to calculate an EEG forward solution with a single-layer BEM.
+
+.. _BABDEEEB:
+
+Setting up the noise-covariance matrix
+######################################
+
+The MNE software employs an estimate of the noise-covariance
+matrix to weight the channels correctly in the calculations. The
+noise-covariance matrix provides information about field and potential
+patterns representing uninteresting noise sources of either human
+or environmental origin.
+
+The noise covariance matrix can be calculated in several
+ways:
+
+- Employ the individual epochs during
+ off-line averaging to calculate the full noise covariance matrix.
+ This is the recommended approach for evoked responses.
+
+- Employ empty room data (collected without the subject) to
+ calculate the full noise covariance matrix. This is recommended
+ for analyzing ongoing spontaneous activity.
+
+- Employ a section of continuous raw data collected in the presence
+ of the subject to calculate the full noise covariance matrix. This
+ is the recommended approach for analyzing epileptic activity. The
+ data used for this purpose should be free of technical artifacts
+ and epileptic activity of interest. The length of the data segment
+ employed should be at least 20 seconds. One can also use a long
+ (> 200 s) segment of data with epileptic spikes present provided
+ that the spikes occur infrequently and that the segment is apparently
+ stationary with respect to background brain activity.
+
+The new raw data processing tools, mne_browse_raw or mne_process_raw include
+computation of noise-covariance matrices both from raw data and
+from individual epochs. For details, see Chapter 4.
+
+.. _CIHCFJEI:
+
+Calculating the inverse operator decomposition
+##############################################
+
+The MNE software doesn't calculate the inverse operator
+explicitly but rather computes an SVD of a matrix composed of the
+noise-covariance matrix, the result of the forward calculation,
+and the source covariance matrix. This approach has the benefit
+that the regularization parameter ('SNR') can
+be adjusted easily when the final source estimates or dSPMs are
+computed. For mathematical details of this approach, please consult Section 6.2.
+
+This computation stage is facilitated by the convenience
+script mne_do_inverse_operator . It
+invokes the program mne_inverse_operator with
+appropriate options, derived from the command line of mne_do_inverse_operator .
+
+mne_do_inverse_operator assumes
+the following options:
+
+**\---fwd <name of the forward solution file>**
+
+ This is the forward solution file produced in the computations step described
+ in :ref:`BABCHEJD`.
+
+**\---meg**
+
+ Employ MEG data in the inverse calculation. If neither ``--meg`` nor ``--eeg`` is
+ set only MEG channels are included.
+
+**\---eeg**
+
+ Employ EEG data in the inverse calculation. If neither ``--meg`` nor ``--eeg`` is
+ set only MEG channels are included.
+
+**\---fixed**
+
+ Use fixed source orientations normal to the cortical mantle. By default,
+ the source orientations are not constrained. If ``--fixed`` is specified,
+ the ``--loose`` flag is ignored.
+
+**\---loose <amount>**
+
+ Use a 'loose' orientation constraint. This means
+ that the source covariance matrix entries corresponding to the current
+ component normal to the cortex are set equal to one and the transverse
+ components are set to <amount> .
+ Recommended value of amount is 0.1...0.6.
+
+**\---depth**
+
+ Employ depth weighting with the standard settings. For details,
+ see Sections 6.2.10 and 6.4.
+
+**\---bad <name>**
+
+ Specifies a text file to designate bad channels, listed one channel name
+ (like MEG 1933) on each line of the file. Be sure to include both
+ noisy and flat (non-functioning) channels in the list. If bad channels
+ were designated using mne_mark_bad_channels in
+ the measurement file which was specified with the ``--meas`` option when
+ the forward solution was computed, the bad channel information will
+ be automatically included. Also, any bad channel information in
+ the noise-covariance matrix file will be included.
+
+**\---noisecov <name>**
+
+ Name of the noise-covariance matrix file computed with one of the methods
+ described in :ref:`BABDEEEB`. By default, the script looks
+ for a file whose name is derived from the forward solution file
+ by replacing its ending ``-`` <anything> ``-fwd.fif`` by ``-cov.fif`` .
+ If this file contains a projection operator, which will automatically
+ attached to the noise-covariance matrix by mne_browse_raw and mne_process_raw ,
+ no ``--proj`` option is necessary because mne_inverse_operator will
+ automatically include the projectors from the noise-covariance matrix
+ file. For backward compatibility, --senscov can be used as a synonym
+ for --noisecov.
+
+**\---noiserank <value>**
+
+ Specifies the rank of the noise covariance matrix explicitly rather than
+ trying to reduce it automatically. This option is sheldom needed,
+
+**\---megreg <value>**
+
+ Regularize the MEG part of the noise-covariance matrix by this amount.
+ Suitable values are in the range 0.05...0.2. For details, see Section 6.2.4.
+
+**\---eegreg <value>**
+
+ Like ``--megreg`` but applies to the EEG channels.
+
+**\---diagnoise**
+
+ Omit the off-diagonal terms of the noise covariance matrix. This option
+ is irrelevant to most users.
+
+**\---fmri <name>**
+
+ With help of this w file, an *a priori* weighting
+ can be applied to the source covariance matrix. The source of the weighting
+ is usually fMRI but may be also some other data, provided that the weighting can
+ be expressed as a scalar value on the cortical surface, stored in
+ a w file. It is recommended that this w file is appropriately smoothed (see Section 8.3)
+ in mne_analyze , tksurfer or
+ with mne_smooth_w to contain
+ nonzero values at all vertices of the triangular tessellation of
+ the cortical surface. The name of the file given is used as a stem of
+ the w files. The actual files should be called <name> ``-lh.pri`` and <name> ``-rh.pri`` for
+ the left and right hemisphere weight files, respectively. The application
+ of the weighting is discussed in Section 6.2.11.
+
+**\---fmrithresh <value>**
+
+ This option is mandatory and has an effect only if a weighting function
+ has been specified with the ``--fmri`` option. If the value
+ is in the *a priori* files falls below this value
+ at a particular source space point, the source covariance matrix
+ values are multiplied by the value specified with the ``--fmrioff`` option
+ (default 0.1). Otherwise it is left unchanged.
+
+**\---fmrioff <value>**
+
+ The value by which the source covariance elements are multiplied
+ if the *a priori* weight falls below the threshold
+ set with ``--fmrithresh`` , see above.
+
+**\---srccov <name>**
+
+ Use this diagonal source covariance matrix. By default the source covariance
+ matrix is a multiple of the identity matrix. This option is irrelevant
+ to most users.
+
+**\---proj <name>**
+
+ Include signal-space projection information from this file.
+
+**\---inv <name>**
+
+ Save the inverse operator decomposition here. By default, the script looks
+ for a file whose name is derived from the forward solution file by
+ replacing its ending ``-fwd.fif`` by <options> ``-inv.fif`` , where
+ <options> includes options --meg, --eeg, and --fixed with the double
+ dashes replaced by single ones.
+
+**\---destdir <directory>**
+
+ Optionally specifies a directory where the inverse operator will
+ be stored.
+
+.. note:: If bad channels are included in the calculation, strange results may ensue. Therefore, it is recommended that the data to be analyzed is carefully inspected with to assign the bad channels correctly.
+
+.. note:: For convenience, the MNE software includes bad-channel designation files which can be used to ignore all magnetometer or all gradiometer channels in Vectorview measurements. These files are called ``vv_grad_only.bad`` and ``vv_mag_only.bad`` , respectively. Both files are located in ``$MNE_ROOT/share/mne/templates`` .
+
+Analyzing the data
+##################
+
+Once all the preprocessing steps described above have been
+completed, the inverse operator computed can be applied to the MEG
+and EEG data and the results can be viewed and stored in several
+ways:
+
+- The interactive analysis tool mne_analyze can
+ be used to explore the data and to produce quantitative analysis
+ results, screen snapshots, and QuickTime (TM) movie files.
+ For comprehensive information on mne_analyze ,
+ please consult Chapter 7.
+
+- The command-line tool mne_make_movie can
+ be invoked to produce QuickTime movies and snapshots. mne_make_movie can
+ also output the data in the stc (movies) and w (snapshots) formats
+ for subsequent processing. Furthermore, subject-to-subject morphing
+ is included in mne_make_movie to
+ facilitate cross-subject averaging and comparison of data among
+ subjects. mne_make_movie is described
+ in Section 6.5,
+
+- The command-line tool mne_make_movie can
+ be employed to interrogate the source estimate waveforms from labels
+ (ROIs).
+
+- The mne_make_movie tool
+ can be also used to create movies from stc files and to resample
+ stc files in time.
+
+- The mne_compute_raw_inverse tool
+ can be used to produce fif files containing source estimates at
+ selected ROIs. The input data file can be either a raw data or evoked
+ response MEG/EEG file, see Section 6.6.
+
+- Using the MNE Matlab toolbox, it is possible to perform many
+ of the above operations in Matlab using your own Matlab code based
+ on the MNE Matlab toolbox. For more information on the MNE Matlab
+ toolbox, see Chapter 10.
+
+- It is also possible to average the source estimates across
+ subjects as described in Chapter 8.
diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst
new file mode 100644
index 0000000..9d65c57
--- /dev/null
+++ b/doc/source/manual/forward.rst
@@ -0,0 +1,1202 @@
+
+
+.. _CBBDEAAI:
+
+====================
+The forward solution
+====================
+
+Overview
+########
+
+This Chapter covers the definitions of different coordinate
+systems employed in MNE software and FreeSurfer, the details of
+the computation of the forward solutions, and the associated low-level
+utilities.
+
+.. _CHDEDFIB:
+
+MEG/EEG and MRI coordinate systems
+##################################
+
+The coordinate systems used in MNE software (and FreeSurfer)
+and their relationships are depicted in :ref:`CHDFFJIJ`.
+Except for the *Sensor coordinates*, all of the
+coordinate systems are Cartesian and have the "RAS" (Right-Anterior-Superior)
+orientation, *i.e.*, the INLINE_EQUATION axis
+points to the right, the INLINE_EQUATION axis
+to the front, and the INLINE_EQUATION axis up.
+
+.. _CHDFFJIJ:
+
+.. figure:: picture.png
+ :alt: none
+
+ MEG/EEG and MRI coordinate systems. The coordinate transforms present in the fif files in MNE and the FreeSurfer files as well as those set to fixed values are indicated with INLINE_EQUATION, where INLINE_EQUATION identifies the transformation.
+
+The coordinate systems related
+to MEG/EEG data are:
+
+**Head coordinates**
+
+ This is a coordinate system defined with help of the fiducial landmarks
+ (nasion and the two auricular points). In fif files, EEG electrode
+ locations are given in this coordinate system. In addition, the head
+ digitization data acquired in the beginning of an MEG, MEG/EEG,
+ or EEG acquisition are expressed in head coordinates. For details,
+ see :ref:`CHDEDFIB`.
+
+**Device coordinates**
+
+ This is a coordinate system tied to the MEG device. The relationship
+ of the Device and Head coordinates is determined during an MEG measurement
+ by feeding current to INLINE_EQUATION head-position
+ indicator (HPI) coils and by determining their locations with respect
+ to the MEG sensor array from the magnetic fields they generate.
+
+**Sensor coordinates**
+
+ Each MEG sensor has a local coordinate system defining the orientation
+ and location of the sensor. With help of this coordinate system,
+ the numerical integration data needed for the computation of the
+ magnetic field can be expressed conveniently as discussed in :ref:`BJEIAEIE`. The channel information data in the fif files
+ contain the information to specify the coordinate transformation
+ between the coordinates of each sensor and the MEG device coordinates.
+
+The coordinate systems related
+to MRI data are:
+
+**Surface RAS coordinates**
+
+ The FreeSurfer surface data are expressed in this coordinate system. The
+ origin of this coordinate system is at the center of the conformed
+ FreeSurfer MRI volumes (usually 256 x 256 x 256 isotropic 1-mm3 voxels)
+ and the axes are oriented along the axes of this volume. The BEM
+ surface and the locations of the sources in the source space are
+ usually expressed in this coordinate system in the fif files. In
+ this manual, the *Surface RAS coordinates* are
+ usually referred to as *MRI coordinates* unless
+ there is need to specifically discuss the different MRI-related
+ coordinate systems.
+
+**RAS coordinates**
+
+ This coordinate system has axes identical to the Surface RAS coordinates but the location of the origin
+ is different and defined by the original MRI data, i.e. ,
+ the origin is in a scanner-dependent location. There is hardly any
+ need to refer to this coordinate system explicitly in the analysis
+ with the MNE software. However, since the Talairach coordinates,
+ discussed below, are defined with respect to *RAS coordinates* rather
+ than the *Surface RAS coordinates*, the RAS coordinate
+ system is implicitly involved in the transformation between Surface RAS coordinates and the two *Talairach* coordinate
+ systems.
+
+**MNI Talairach coordinates**
+
+ The definition of this coordinate system is discussed, e.g. ,
+ in http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach. This
+ transformation is determined during the FreeSurfer reconstruction
+ process.
+
+**FreeSurfer Talairach coordinates**
+
+ The problem with the MNI Talairach coordinates is that the linear MNI
+ Talairach transform does matched the brains completely to the Talairach
+ brain. This is probably because the Talairach atlas brain is a rather
+ odd shape, and as a result, it is difficult to match a standard brain
+ to the atlas brain using an affine transform. As a result, the MNI
+ brains are slightly larger (in particular higher, deeper and longer)
+ than the Talairach brain. The differences are larger as you get
+ further from the middle of the brain, towards the outside. The FreeSurfer
+ Talairach coordinates mitigate this problem by additing a an additional
+ transformation, defined separately for negatice and positive MNI
+ Talairach INLINE_EQUATION coordinates. These two
+ transformations, denoted by INLINE_EQUATION and INLINE_EQUATION in :ref:`CHDFFJIJ`, are fixed as discussed in http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach
+ (*Approach 2*).
+
+The different coordinate systems are related by coordinate
+transformations depicted in :ref:`CHDFFJIJ`. The arrows and
+coordinate transformation symbols (INLINE_EQUATION)
+indicate the transformations actually present in the FreeSurfer
+files. Generally,
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION are the location
+coordinates in two coordinate systems, INLINE_EQUATION is
+the coordinate transformation from coordinate system "1" to "2",
+INLINE_EQUATION is the location of the origin
+of coordinate system "1" in coordinate system"2",
+and INLINE_EQUATION are the elements of the rotation
+matrix relating the two coordinate systems. The coordinate transformations
+are present in different files produced by FreeSurfer and MNE as
+summarized in :ref:`CHDJDEDJ`. The fixed transformations INLINE_EQUATION and INLINE_EQUATION are:
+
+.. math:: 1 + 1 = 2
+
+and
+
+.. math:: 1 + 1 = 2
+
+.. note:: This section does not discuss the transformation between the MRI voxel indices and the different MRI coordinates. However, it is important to note that in FreeSurfer, MNE, as well as in Neuromag software an integer voxel coordinate corresponds to the location of the center of a voxel. Detailed information on the FreeSurfer MRI systems can be found at https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems.
+
+.. _CHDJDEDJ:
+
+.. table:: Coordinate transformations in FreeSurfer and MNE software packages. The symbols INLINE_EQUATION are defined in :ref:`CHDFFJIJ` Note: mne_make_cor_set /mne_setup_mri prior to release 2.6 did not include transformations INLINE_EQUATION, INLINE_EQUATION, INLINE_EQUATION, and INLINE_EQUATION in the fif files produced.).
+
+ ================== =============================== =======================================================================================================================================
+ Transformation FreeSurfer MNE
+ ================== =============================== =======================================================================================================================================
+ INLINE_EQUATION Not present Measurement data files Forward solution files \fwd.fif) Inverse operator files \inv.fif)
+ INLINE_EQUATION Not present Channel information in files containing INLINE_EQUATION.
+ INLINE_EQUATION Not present MRI description files Separate coordinate transformation files saved from mne_analyze Forward solution files Inverse operator files
+ INLINE_EQUATION mri\mgz files MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format.
+ INLINE_EQUATION mri/transforms/talairach.xfm MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format.
+ INLINE_EQUATION Hardcoded in software MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format.
+ INLINE_EQUATION Hardcoded in software MRI description files saved with mne_make_cor_set if the input is in mgz or mgh format.
+ ================== =============================== =======================================================================================================================================
+
+.. _BJEBIBAI:
+
+The head and device coordinate systems
+######################################
+
+.. figure:: picture.png
+ :alt: none
+
+ The head coordinate system
+
+The MEG/EEG head coordinate system employed in the MNE software
+is a right-handed Cartesian coordinate system. The direction of INLINE_EQUATION axis
+is from left to right, that of INLINE_EQUATION axis
+to the front, and the INLINE_EQUATION axis thus
+points up.
+
+The INLINE_EQUATION axis of the head coordinate
+system passes through the two periauricular or preauricular points
+digitized before acquiring the data with positive direction to the
+right. The INLINE_EQUATION axis passes through
+the nasion and is normal to the INLINE_EQUATION axis.
+The INLINE_EQUATION axis points up according to
+the right-hand rule and is normal to the INLINE_EQUATION plane.
+
+The origin of the MEG device coordinate system is device
+dependent. Its origin is located approximately at the center of
+a sphere which fits the occipital section of the MEG helmet best
+with INLINE_EQUATION axis going from left to right
+and INLINE_EQUATION axis pointing front. The INLINE_EQUATION axis
+is, again normal to the INLINE_EQUATION plane
+with positive direction up.
+
+.. note:: The above definition is identical to that of the Neuromag MEG/EEG (head) coordinate system. However, in 4-D Neuroimaging and CTF MEG systems the head coordinate frame definition is different. The origin of the coordinate system is at the midpoint of the left and right auricular points. The INLINE_EQUATION axis passes through the nasion and the origin with positive direction to the front. The INLINE_EQUATION axis is perpendicular to the INLINE_EQUATION axis [...]
+
+.. _BEHCGJDD:
+
+Creating a surface-based source space
+#####################################
+
+The fif format source space files containing the dipole locations
+and orientations are created with the utility mne_make_source_space .
+This utility is usually invoked by the convenience script mne_setup_source_space ,
+see Section 3.5.
+
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---subject <name>**
+
+ Name of the subject in SUBJECTS_DIR. In the absense of this option,
+ the SUBJECT environment variable will be consulted. If it is not
+ defined, mne_setup_source_space exits
+ with an error.
+
+**\---morph <name>**
+
+ Name of a subject in SUBJECTS_DIR. If this option is present, the source
+ space will be first constructed for the subject defined by the --subject
+ option or the SUBJECT environment variable and then morphed to this
+ subject. This option is useful if you want to create a source spaces
+ for several subjects and want to directly compare the data across
+ subjects at the source space vertices without any morphing procedure
+ afterwards. The drawback of this approach is that the spacing between
+ source locations in the "morph" subject is not going
+ to be as uniform as it would be without morphing.
+
+**\---surf <name1>:<name2>:...**
+
+ FreeSurfer surface file names specifying the source surfaces, separated
+ by colons.
+
+**\---spacing <spacing/mm>**
+
+ Specifies the approximate grid spacing of the source space in mm.
+
+**\---ico <number>**
+
+ Instead of using the traditional method for cortical surface decimation
+ it is possible to create the source space using the topology of
+ a recursively subdivided icosahedron (<number> > 0)
+ or an octahedron (<number> < 0).
+ This method uses the cortical surface inflated to a sphere as a
+ tool to find the appropriate vertices for the source space. The
+ benefit of the --ico option is that the source space will have triangulation
+ information between the decimated vertices included, which some
+ future versions of MNE software may be able to utilize. The number
+ of triangles increases by a factor of four in each subdivision,
+ starting from 20 triangles in an icosahedron and 8 triangles in
+ an octahedron. Since the number of vertices on a closed surface
+ is INLINE_EQUATION, the number of vertices in
+ the *k*th subdivision of an icosahedron and an
+ octahedron are INLINE_EQUATION and INLINE_EQUATION,
+ respectively. The recommended values for <number> and
+ the corresponding number of source space locations are listed in Table 3.1.
+
+**\---all**
+
+ Include all nodes to the output. The active dipole nodes are identified
+ in the fif file by a separate tag. If tri files were used as input
+ the output file will also contain information about the surface
+ triangulation. This option is always recommended to include complete
+ information.
+
+**\---src <name>**
+
+ Output file name. Use a name *<dir>/<name>*-src.fif
+
+.. note:: If both ``--ico`` and ``--spacing`` options are present the later one on the command line takes precedence.
+
+.. note:: Due to the differences between the FreeSurfer and MNE libraries, the number of source space points generated with the ``--spacing`` option may be different between the current version of MNE and versions 2.5 or earlier (using ``--spacing`` option to mne_setup_source_space ) if the FreeSurfer surfaces employ the (old) quadrangle format or if there are topological defects on the surfaces. All new FreeSurfer surfaces are specified as triangular tessellations a [...]
+
+.. _BJEFEHJI:
+
+Creating a volumetric or discrete source space
+##############################################
+
+In addition to source spaces confined to a surface, the MNE
+software provides some support for three-dimensional source spaces
+bounded by a surface as well as source spaces comprised of discrete,
+arbitrarily located source points. The mne_volume_source_space utility
+assists in generating such source spaces.
+
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---surf <name>**
+
+ Specifies a FreeSurfer surface file containing the surface which
+ will be used as the boundary for the source space.
+
+**\---bem <name>**
+
+ Specifies a BEM file (ending in ``-bem.fif`` ). The inner
+ skull surface will be used as the boundary for the source space.
+
+**\---origin <x/mm> :<y/mm> :<z/mm>**
+
+ If neither of the two surface options described above is present,
+ the source space will be spherical with the origin at this location,
+ given in MRI (RAS) coordinates.
+
+**\---rad <radius/mm>**
+
+ Specifies the radius of a spherical source space. Default value
+ = 90 mm
+
+**\---grid <spacing/mm>**
+
+ Specifies the grid spacing in the source space.
+
+**\---mindist <distance/mm>**
+
+ Only points which are further than this distance from the bounding surface
+ are included. Default value = 5 mm.
+
+**\---exclude <distance/mm>**
+
+ Exclude points that are closer than this distance to the center
+ of mass of the bounding surface. By default, there will be no exclusion.
+
+**\---mri <name>**
+
+ Specifies a MRI volume (in mgz or mgh format).
+ If this argument is present the output source space file will contain
+ a (sparse) interpolation matrix which allows mne_volume_data2mri to
+ create an MRI overlay file, see Section 9.4.
+
+**\---pos <name>**
+
+ Specifies a name of a text file containing the source locations
+ and, optionally, orientations. Each line of the file should contain
+ 3 or 6 values. If the number of values is 3, they indicate the source
+ location, in millimeters. The orientation of the sources will be
+ set to the z-direction. If the number of values is 6, the source
+ orientation will be parallel to the vector defined by the remaining
+ 3 numbers on each line. With ``--pos`` , all of the options
+ defined above will be ignored. By default, the source position and
+ orientation data are assumed to be given in MRI coordinates.
+
+**\---head**
+
+ If this option is present, the source locations and orientations
+ in the file specified with the ``--pos`` option are assumed
+ to be given in the MEG head coordinates.
+
+**\---meters**
+
+ Indicates that the source locations in the file defined with the ``--pos`` option
+ are give in meters instead of millimeters.
+
+**\---src <name>**
+
+ Specifies the output file name. Use a name *<dir>/<name>*-src.fif
+
+**\---all**
+
+ Include all vertices in the output file, not just those in use.
+ This option is implied when the ``--mri`` option is present.
+ Even with the ``--all`` option, only those vertices actually
+ selected will be marked to be "in use" in the
+ output source space file.
+
+.. _BEHCACCJ:
+
+Creating the BEM meshes
+#######################
+
+The mne_surf2bem utility
+converts surface triangle meshes from ASCII and FreeSurfer binary
+file formats to the fif format. The resulting fiff file also contains
+conductivity information so that it can be employed in the BEM calculations.
+
+.. note:: The utility mne_tri2fiff previously used for this task has been replaced by mne_surf2bem .
+
+.. note:: The convenience script mne_setup_forward_model described in Section 3.7 calls mne_surf2bem with the appropriate options.
+
+.. note:: The vertices of all surfaces should be given in the MRI coordinate system.
+
+Command-line options
+====================
+
+This program has the following
+command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---surf <name>**
+
+ Specifies a FreeSurfer binary format surface file. Before specifying the
+ next surface (``--surf`` or ``--tri`` options)
+ details of the surface specification can be given with the options
+ listed in :ref:`BEHCDICC`.
+
+**\---tri <name>**
+
+ Specifies a text format surface file. Before specifying the next
+ surface (``--surf`` or ``--tri`` options) details
+ of the surface specification can be given with the options listed
+ in :ref:`BEHCDICC`. The format of these files is described
+ in :ref:`BEHDEFCD`.
+
+**\---check**
+
+ Check that the surfaces are complete and that they do not intersect. This
+ is a recommended option. For more information, see :ref:`BEHCBDDE`.
+
+**\---checkmore**
+
+ In addition to the checks implied by the ``--check`` option,
+ check skull and skull thicknesses. For more information, see :ref:`BEHCBDDE`.
+
+**\---fif <name>**
+
+ The output fif file containing the BEM. These files normally reside in
+ the bem subdirectory under the subject's mri data. A name
+ ending with ``-bem.fif`` is recommended.
+
+.. _BEHCDICC:
+
+Surface options
+===============
+
+These options can be specified after each ``--surf`` or ``--tri`` option
+to define details for the corresponding surface.
+
+**\---swap**
+
+ Swap the ordering or the triangle vertices. The standard convention in
+ the MNE software is to have the vertices ordered so that the vector
+ cross product of the vectors from vertex 1 to 2 and 1 to 3 gives the
+ direction of the outward surface normal. Text format triangle files
+ produced by the some software packages have an opposite order. For
+ these files, the ``--swap`` . option is required. This option does
+ not have any effect on the interpretation of the FreeSurfer surface
+ files specified with the ``--surf`` option.
+
+**\---sigma <value>**
+
+ The conductivity of the compartment inside this surface in S/m.
+
+**\---shift <value/mm>**
+
+ Shift the vertices of this surface by this amount, given in mm,
+ in the outward direction, *i.e.*, in the positive
+ vertex normal direction.
+
+**\---meters**
+
+ The vertex coordinates of this surface are given in meters instead
+ of millimeters. This option applies to text format files only. This
+ definition does not affect the units of the shift option.
+
+**\---id <number>**
+
+ Identification number to assign to this surface. (1 = inner skull, 3
+ = outer skull, 4 = scalp).
+
+**\---ico <number>**
+
+ Downsample the surface to the designated subdivision of an icosahedron.
+ This option is relevant (and required) only if the triangulation
+ is isomorphic with a recursively subdivided icosahedron. For example,
+ the surfaces produced by with mri_watershed are
+ isomorphic with the 5th subdivision of a an icosahedron thus containing 20480
+ triangles. However, this number of triangles is too large for present
+ computers. Therefore, the triangulations have to be decimated. Specifying ``--ico 4`` yields 5120 triangles per surface while ``--ico 3`` results
+ in 1280 triangles. The recommended choice is ``--ico 4`` .
+
+.. _BEHDEFCD:
+
+Tessellation file format
+========================
+
+The format of the text format surface files is the following:
+
+<nvert> <vertex 1> <vertex 2>
+...<vertex nvert> <ntri> <triangle 1> <triangle 2>
+...<triangle ntri> ,
+
+where <nvert> and <ntri> are
+the number of vertices and number of triangles in the tessellation,
+respectively.
+
+The format of a vertex entry is
+one of the following:
+
+**x y z**
+
+ The x, y, and z coordinates of the vertex location are given in
+ mm.
+
+**number x y z**
+
+ A running number and the x, y, and z coordinates are given. The running
+ number is not considered by mne_tri2fiff. The nodes must be thus
+ listed in the correct consecutive order.
+
+**x y z nx ny nz**
+
+ The x, y, and z coordinates as well as the approximate vertex normal direction
+ cosines are given.
+
+**number x y z nx ny nz**
+
+ A running number is given in addition to the vertex location and vertex
+ normal.
+
+Each triangle entry consists of the numbers of the vertices
+belonging to a triangle. The vertex numbering starts from one. The
+triangle list may also contain running numbers on each line describing
+a triangle.
+
+.. _BEHCBDDE:
+
+Topology checks
+===============
+
+If the ``--check`` option is specified, the following
+topology checks are performed:
+
+- The completeness of each surface is
+ confirmed by calculating the total solid angle subtended by all
+ triangles from a point inside the triangulation. The result should
+ be very close to INLINE_EQUATION. If the result
+ is INLINE_EQUATION instead, it is conceivable
+ that the ordering of the triangle vertices is incorrect and the
+ --swap option should be specified.
+
+- The correct ordering of the surfaces is verified by checking
+ that the surfaces are inside each other as expected. This is accomplished
+ by checking that the sum solid angles subtended by triangles of
+ a surface INLINE_EQUATION at all vertices of another
+ surface INLINE_EQUATION which is supposed to be
+ inside it equals INLINE_EQUATION. Naturally, this
+ check is applied only if the model has more than one surface. Since
+ the surface relations are transitive, it is enough to check that
+ the outer skull surface is inside the skin surface and that the
+ inner skull surface is inside the outer skull one.
+
+- The extent of each of the triangulated volumes is checked.
+ If the extent is smaller than 50 mm, an error is reported. This
+ may indicate that the vertex coordinates have been specified in
+ meters instead of millimeters.
+
+.. _CHDJFHEB:
+
+Computing the BEM geometry data
+###############################
+
+The utility mne_prepare_bem_model computes
+the geometry information for BEM. This utility is usually invoked
+by the convenience script mne_setup_forward_model ,
+see Section 3.7. The command-line options are:
+
+**\---bem <name>**
+
+ Specify the name of the file containing the triangulations of the BEM
+ surfaces and the conductivities of the compartments. The standard
+ ending for this file is ``-bem.fif`` and it is produced
+ either with the utility mne_surf2bem (:ref:`BEHCACCJ`) or the convenience script mne_setup_forward_model ,
+ see Section 3.7.
+
+**\---sol <name>**
+
+ Specify the name of the file containing the triangulation and conductivity
+ information together with the BEM geometry matrix computed by mne_prepare_bem_model .
+ The standard ending for this file is ``-bem-sol.fif`` .
+
+**\---method <approximation method>**
+
+ Select the BEM approach. If <approximation method> is ``constant`` ,
+ the BEM basis functions are constant functions on each triangle
+ and the collocation points are the midpoints of the triangles. With ``linear`` ,
+ the BEM basis functions are linear functions on each triangle and
+ the collocation points are the vertices of the triangulation. This
+ is the preferred method to use. The accuracy will be the same or
+ better than in the constant collocation approach with about half
+ the number of unknowns in the BEM equations.
+
+.. _BJEIAEIE:
+
+Coil geometry information
+#########################
+
+This Section explains the presentation of MEG detection coil
+geometry information the approximations used for different detection
+coils in MNE software. Two pieces of information are needed to characterize
+the detectors:
+
+- The location and orientation a local
+ coordinate system for each detector.
+
+- A unique identifier, which has an one-to-one correspondence
+ to the geometrical description of the coil.
+
+The sensor coordinate system
+============================
+
+The sensor coordinate system is completely characterized
+by the location of its origin and the direction cosines of three
+orthogonal unit vectors pointing to the directions of the x, y,
+and z axis. In fact, the unit vectors contain redundant information
+because the orientation can be uniquely defined with three angles.
+The measurement fif files list these data in MEG device coordinates.
+Transformation to the MEG head coordinate frame can be easily accomplished
+by applying the device-to-head coordinate transformation matrix
+available in the data files provided that the head-position indicator
+was used. Optionally, the MNE software forward calculation applies
+another coordinate transformation to the head-coordinate data to
+bring the coil locations and orientations to the MRI coordinate system.
+
+If INLINE_EQUATION is a row vector for
+the origin of the local sensor coordinate system and INLINE_EQUATION, INLINE_EQUATION,
+and INLINE_EQUATION are the row vectors for the
+three orthogonal unit vectors, all given in device coordinates,
+a location of a point INLINE_EQUATION in sensor coordinates
+is transformed to device coordinates (INLINE_EQUATION)
+by
+
+.. math:: 1 + 1 = 2
+
+where
+
+.. math:: 1 + 1 = 2
+
+Calculation of the magnetic field
+=================================
+
+The forward calculation in the MNE software computes the
+signals detected by each MEG sensor for three orthogonal dipoles
+at each source space location. This requires specification of the
+conductor model, the location and orientation of the dipoles, and
+the location and orientation of each MEG sensor as well as its coil
+geometry.
+
+The output of each SQUID sensor is a weighted sum of the
+magnetic fluxes threading the loops comprising the detection coil.
+Since the flux threading a coil loop is an integral of the magnetic
+field component normal to the coil plane, the output of the *k*th
+MEG channel, INLINE_EQUATION, can be approximated
+by:
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION are a set of INLINE_EQUATION integration
+points covering the pickup coil loops of the sensor, INLINE_EQUATION is
+the magnetic field due to the current sources calculated at INLINE_EQUATION, INLINE_EQUATION are
+the coil normal directions at these points, and INLINE_EQUATION are
+the weights associated to the integration points. This formula essentially
+presents numerical integration of the magnetic field over the pickup
+loops of sensor INLINE_EQUATION.
+
+There are three accuracy levels for the numerical integration
+expressed above. The *simple* accuracy means
+the simplest description of the coil. This accuracy is not used
+in the MNE forward calculations. The *normal* or *recommended* accuracy typically uses
+two integration points for planar gradiometers, one in each half
+of the pickup coil and four evenly distributed integration points
+for magnetometers. This is the default accuracy used by MNE. If
+the ``--accurate`` option is specified, the forward calculation typically employs
+a total of eight integration points for planar gradiometers and
+sixteen for magnetometers. Detailed information about the integration
+points is given in the next section.
+
+Implemented coil geometries
+===========================
+
+This section describes the coil geometries currently implemented
+in Neuromag software. The coil types fall in two general categories:
+
+- Axial gradiometers and planar gradiometers
+ and
+
+- Planar gradiometers.
+
+For axial sensors, the *z* axis of the
+local coordinate system is parallel to the field component detected, *i.e.*,
+normal to the coil plane.For circular coils, the orientation of
+the *x* and *y* axes on the
+plane normal to the z axis is irrelevant. In the square coils employed
+in the Vectorview (TM) system the *x* axis
+is chosen to be parallel to one of the sides of the magnetometer
+coil. For planar sensors, the *z* axis is likewise
+normal to the coil plane and the x axis passes through the centerpoints
+of the two coil loops so that the detector gives a positive signal
+when the normal field component increases along the *x* axis.
+
+:ref:`BGBBHGEC` lists the parameters of the *normal* coil
+geometry descriptions :ref:`CHDBDFJE` lists the *accurate* descriptions. For simple accuracy,
+please consult the coil definition file, see :ref:`BJECIGEB`.
+The columns of the tables contain the following data:
+
+- The number identifying the coil id.
+ This number is used in the coil descriptions found in the FIF files.
+
+- Description of the coil.
+
+- Number of integration points used
+
+- The locations of the integration points in sensor coordinates.
+
+- Weights assigned to the field values at the integration points.
+ Some formulas are listed instead of the numerical values to demonstrate
+ the principle of the calculation. For example, in the normal coil
+ descriptions of the planar gradiometers the weights are inverses
+ of the baseline of the gradiometer to show that the output is in
+ T/m.
+
+.. note:: The coil geometry information is stored in the file $MNE_ROOT/share/mne/coil_def.dat, which is automatically created by the utility mne_list_coil_def , see :ref:`BJEHHJIJ`.
+
+.. _BGBBHGEC:
+
+.. table:: Normal coil descriptions. Note: If a plus-minus sign occurs in several coordinates, all possible combinations have to be included.
+
+ ======= ================================================================ ==== =============================================================== ===============================================================
+ Id Description n r/mm w
+ ======= ================================================================ ==== =============================================================== ===============================================================
+ 2 Neuromag-122 planar gradiometer 2 INLINE_EQUATION INLINE_EQUATION
+ 2000 A point magnetometer 1 INLINE_EQUATION 1
+ 3012 Vectorview type 1 planar gradiometer 2 INLINE_EQUATION INLINE_EQUATION
+ 3013 Vectorview type 2 planar gradiometer 2 INLINE_EQUATION INLINE_EQUATION
+ 3022 Vectorview type 1 magnetometer 4 INLINE_EQUATION INLINE_EQUATION
+ 3023 Vectorview type 2 magnetometer 4 INLINE_EQUATION INLINE_EQUATION
+ 3024 Vectorview type 3 magnetometer 4 INLINE_EQUATION INLINE_EQUATION
+ 2000 An ideal point magnetometer 1 (0,0,0) 1
+ 4001 Magnes WH magnetometer 4 INLINE_EQUATION INLINE_EQUATION
+ 4002 Magnes WH 3600 axial gradiometer 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION
+ 4003 Magnes reference magnetometer 4 INLINE_EQUATION INLINE_EQUATION
+ 4004 Magnes reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION
+ 4005 Magnes reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION
+ 5001 CTF 275 axial gradiometer 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION
+ 5002 CTF reference magnetometer 4 INLINE_EQUATION INLINE_EQUATION
+ 5003 CTF reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION
+ 5004 CTF reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION
+ 6001 MIT KIT system axial gradiometer 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION
+ ======= ================================================================ ==== =============================================================== ===============================================================
+
+.. _CHDBDFJE:
+
+.. table:: Accurate coil descriptions
+
+ ======= ================================================================ ===== ============================================================================================= =============================================================================================
+ Id Description n r/mm w
+ ======= ================================================================ ===== ============================================================================================= =============================================================================================
+ 2 Neuromag-122 planar gradiometer 8 INLINE_EQUATION,INLINE_EQUATION INLINE_EQUATION
+ 2000 A point magnetometer 1 INLINE_EQUATION 1
+ 3012 Vectorview type 1 planar gradiometer 8 INLINE_EQUATION,INLINE_EQUATION INLINE_EQUATION
+ 3013 Vectorview type 2 planar gradiometer 8 INLINE_EQUATION,INLINE_EQUATION INLINE_EQUATION
+ 3022 Vectorview type 1 magnetometer 16 INLINE_EQUATION,INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATION
+ 3023 Vectorview type 2 magnetometer 16 INLINE_EQUATION,INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATION
+ 3024 Vectorview type 3 magnetometer 16 INLINE_EQUATION,INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATION
+ 4001 Magnes WH magnetometer 7 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION
+ 4002 Magnes WH 3600 axial gradiometer 14 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION
+ 4004 Magnes reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION
+ 4005 Magnes reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION
+ 4004 Magnes reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION
+ 5001 CTF 275 axial gradiometer 14 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION
+ 5002 CTF reference magnetometer 4 INLINE_EQUATION INLINE_EQUATION
+ 5003 CTF reference gradiometer measuring diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATION
+ 5004 CTF reference gradiometer measuring off-diagonal gradients 8 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION
+ 6001 MIT KIT system axial gradiometer 14 INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION INLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATIONINLINE_EQUATION
+ ======= ================================================================ ===== ============================================================================================= =============================================================================================
+
+.. _BJECIGEB:
+
+The coil definition file
+========================
+
+The coil geometry information is stored in the text file
+$MNE_ROOT/share/mne/coil_def.dat. In this file, any lines starting
+with the pound sign (#) are comments. A coil definition starts with
+a description line containing the following fields:
+
+**<class>**
+
+ This is a number indicating class of this coil. Possible values
+ are listed in :ref:`BJEFABHA`.
+
+**<id>**
+
+ Coil id value. This value is listed in the first column of Tables :ref:`BGBBHGEC` and :ref:`CHDBDFJE`.
+
+**<accuracy>**
+
+ The coil representation accuracy. Possible values and their meanings
+ are listed in :ref:`BJEHIBJC`.
+
+**<np>**
+
+ Number of integration points in this representation.
+
+**<size/m>**
+
+ The size of the coil. For circular coils this is the diameter of
+ the coil and for square ones the side length of the square. This
+ information is mainly included to facilitate drawing of the coil
+ geometry. It should not be employed to infer a coil approximation
+ for the forward calculations.
+
+**<baseline/m>**
+
+ The baseline of a this kind of a coil. This will be zero for magnetometer
+ coils. This information is mainly included to facilitate drawing
+ of the coil geometry. It should not be employed to infer a coil
+ approximation for the forward calculations.
+
+**<description>**
+
+ Short description of this kind of a coil. If the description contains several
+ words, it is enclosed in quotes.
+
+.. _BJEFABHA:
+
+.. table:: Coil class values
+
+ ======= =======================================================
+ Value Meaning
+ ======= =======================================================
+ 1 magnetometer
+ 2 first-order axial gradiometer
+ 3 planar gradiometer
+ 4 second-order axial gradiometer
+ 1000 an EEG electrode (used internally in software only).
+ ======= =======================================================
+
+.. _BJEHIBJC:
+
+.. table:: Coil representation accuracies.
+
+ ======= =====================================================================
+ Value Meaning
+ ======= =====================================================================
+ 1 The simplest representation available
+ 2 The standard or *normal* representation (see :ref:`BGBBHGEC`)
+ 3 The most *accurate* representation available (see :ref:`CHDBDFJE`)
+ ======= =====================================================================
+
+Each coil description line is followed by one or more integration
+point lines, consisting of seven numbers:
+
+**<weight>**
+
+ Gives the weight for this integration point (last column in Tables :ref:`BGBBHGEC` and :ref:`CHDBDFJE`).
+
+**<x/m> <y/m> <z/m>**
+
+ Indicates the location of the integration point (fourth column in Tables :ref:`BGBBHGEC` and :ref:`CHDBDFJE`).
+
+**<nx> <ny> <nz>**
+
+ Components of a unit vector indicating the field component to be selected.
+ Note that listing a separate unit vector for each integration points
+ allows the implementation of curved coils and coils with the gradiometer
+ loops tilted with respect to each other.
+
+.. _BJEHHJIJ:
+
+Creating the coil definition file
+=================================
+
+The standard coil definition file $MNE_ROOT/share/mne/coil_def.dat
+is included with the MNE software package. The coil definition file
+can be recreated with the utility mne_list_coil_def
+as follows:
+
+mne_list_coil_def --out $MNE_ROOT/share/mne/coil_def.dat
+
+.. _CHDDIBAH:
+
+Computing the forward solution
+##############################
+
+Purpose
+=======
+
+Instead of using the convenience script mne_do_forward_solution it
+is also possible to invoke the forward solution computation program mne_forward_solution directly.
+In this approach, the convenience of the automatic file naming conventions
+present in mne_do_forward_solution are
+lost. However, there are some special-purpose options available
+in mne_forward_solution only.
+Please refer to Section 3.11 for information on mne_do_forward_solution .
+
+.. _BJEIGFAE:
+
+Command line options
+====================
+
+mne_forward_solution accepts
+the following command-line options:
+
+**\---src <name>**
+
+ Source space name to use. The name of the file must be specified exactly,
+ including the directory. Typically, the source space files reside
+ in $SUBJECTS_DIR/$SUBJECT/bem.
+
+**\---bem <name>**
+
+ Specifies the BEM to be used. These files end with bem.fif or bem-sol.fif and
+ reside in $SUBJECTS_DIR/$SUBJECT/bem. The former file contains only
+ the BEM surface information while the latter files contain the geometry
+ information precomputed with mne_prepare_bem_model ,
+ see :ref:`CHDJFHEB`. If precomputed geometry is not available,
+ the linear collocation solution will be computed by mne_forward_solution .
+
+**\---origin <x/mm> :<x/mm> :<z/mm>**
+
+ Indicates that the sphere model should be used in the forward calculations.
+ The origin is specified in MEG head coordinates unless the ``--mricoord`` option
+ is present. The MEG sphere model solution computed using the analytical
+ Sarvas formula. For EEG, an approximative solution described in
+
+**\---eegmodels <name>**
+
+ This option is significant only if the sphere model is used and
+ EEG channels are present. The specified file contains specifications
+ of the EEG sphere model layer structures as detailed in :ref:`CHDIAFIG`. If this option is absent the file ``$HOME/.mne/EEG_models`` will
+ be consulted if it exists.
+
+**\---eegmodel <model name>**
+
+ Specifies the name of the sphere model to be used for EEG. If this option
+ is missing, the model Default will
+ be employed, see :ref:`CHDIAFIG`.
+
+**\---eegrad <radius/mm>**
+
+ Specifies the radius of the outermost surface (scalp) of the EEG sphere
+ model, see :ref:`CHDIAFIG`. The default value is 90 mm.
+
+**\---eegscalp**
+
+ Scale the EEG electrode locations to the surface of the outermost sphere
+ when using the sphere model.
+
+**\---accurate**
+
+ Use accurate MEG sensor coil descriptions. This is the recommended
+ choice. More information
+
+**\---fixed**
+
+ Compute the solution for sources normal to the cortical mantle only. This
+ option should be used only for surface-based and discrete source
+ spaces.
+
+**\---all**
+
+ Compute the forward solution for all vertices on the source space.
+
+**\---label <name>**
+
+ Compute the solution only for points within the specified label. Multiple
+ labels can be present. The label files should end with ``-lh.label`` or ``-rh.label`` for
+ left and right hemisphere label files, respectively. If ``--all`` flag
+ is present, all surface points falling within the labels are included.
+ Otherwise, only decimated points with in the label are selected.
+
+**\---mindist <dist/mm>**
+
+ Omit source space points closer than this value to the inner skull surface.
+ Any source space points outside the inner skull surface are automatically
+ omitted. The use of this option ensures that numerical inaccuracies
+ for very superficial sources do not cause unexpected effects in
+ the final current estimates. Suitable value for this parameter is
+ of the order of the size of the triangles on the inner skull surface.
+ If you employ the seglab software to create the triangulations, this
+ value should be about equal to the wish for the side length of the
+ triangles.
+
+**\---mindistout <name>**
+
+ Specifies a file name to contain the coordinates of source space points
+ omitted due to the ``--mindist`` option.
+
+**\---mri <name>**
+
+ The name of the MRI description file containing the MEG/MRI coordinate
+ transformation. This file was saved as part of the alignment procedure
+ outlined in Section 3.10. These files typically reside in ``$SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets`` .
+
+**\---trans <name>**
+
+ The name of a text file containing the 4 x 4 matrix for the coordinate transformation
+ from head to mri coordinates. With --trans, --mri option is not
+ required.
+
+**\---notrans**
+
+ The MEG/MRI coordinate transformation is taken as the identity transformation, *i.e.*,
+ the two coordinate systems are the same. This option is useful only
+ in special circumstances. If more than one of the ``--mri`` , ``--trans`` ,
+ and ``--notrans`` options are specified, the last one remains
+ in effect.
+
+**\---mricoord**
+
+ Do all computations in the MRI coordinate system. The forward solution
+ matrix is not affected by this option if the source orientations
+ are fixed to be normal to the cortical mantle. If all three source components
+ are included, the forward three source orientations parallel to
+ the coordinate axes is computed. If ``--mricoord`` is present, these
+ axes correspond to MRI coordinate system rather than the default
+ MEG head coordinate system. This option is useful only in special
+ circumstances.
+
+**\---meas <name>**
+
+ This file is the measurement fif file or an off-line average file
+ produced thereof. It is recommended that the average file is employed for
+ evoked-response data and the original raw data file otherwise. This
+ file provides the MEG sensor locations and orientations as well as
+ EEG electrode locations as well as the coordinate transformation between
+ the MEG device coordinates and MEG head-based coordinates.
+
+**\---fwd <name>**
+
+ This file will contain the forward solution as well as the coordinate transformations,
+ sensor and electrode location information, and the source space
+ data. A name of the form <name>-fwd.fif is
+ recommended.
+
+**\---meg**
+
+ Compute the MEG forward solution.
+
+**\---eeg**
+
+ Compute the EEG forward solution.
+
+**\---grad**
+
+ Include the derivatives of the fields with respect to the dipole
+ position coordinates to the output, see :ref:`BJEFEJJG`.
+
+Implementation of software gradient compensation
+================================================
+
+As described in Section 9.2.4 the CTF and 4D Neuroimaging
+data may have been subjected to noise cancellation employing the
+data from the reference sensor array. Even though these sensor are
+rather far away from the brain sources, mne_forward_solution takes
+them into account in the computations. If the data file specified
+with the ``--meas`` option has software gradient compensation
+activated, mne_forward_solution computes
+the field of at the reference sensors in addition to the main MEG
+sensor array and computes a compensated forward solution using the
+methods descibed in Section 9.2.4.
+
+.. warning:: If a data file specified with the ``--meas`` option and that used in the actual inverse computations with mne_analyze and mne_make_movie have different software gradient compensation states., the forward solution will be in mismatch with the data to be analyzed and the current estimates will be slightly erroneous.
+
+.. _CHDIAFIG:
+
+The EEG sphere model definition file
+====================================
+
+For the computation of the electric potential distribution
+on the surface of the head (EEG) it is necessary to define the conductivities
+(INLINE_EQUATION) and radiuses of the spherically
+symmetric layers. Different sphere models can be specified with
+the ``--eegmodels`` option.
+
+The EEG sphere model definition files may contain comment
+lines starting with a # and model
+definition lines in the following format:
+
+<name>:<radius1>:<conductivity1>:<radius2>:<conductivity2>:...
+
+When the file is loaded the layers are sorted so that the
+radiuses will be in ascending order and the radius of the outermost
+layer is scaled to 1.0. The scalp radius specified with the ``--eegrad`` option
+is then consulted to scale the model to the correct dimensions.
+Even if the model setup file is not present, a model called Default is
+always provided. This model has the structure given in :ref:`BABEBGDA`
+
+.. _BABEBGDA:
+
+.. table:: Structure of the default EEG model
+
+ ======== ======================= =======================
+ Layer Relative outer radius INLINE_EQUATION (S/m)
+ ======== ======================= =======================
+ Head 1.0 0.33
+ Skull 0.97 0.04
+ CSF 0.92 1.0
+ Brain 0.90 0.33
+ ======== ======================= =======================
+
+EEG forward solution in the sphere model
+========================================
+
+When the sphere model is employed, the computation of the
+EEG solution can be substantially accelerated by using approximation
+methods described by Mosher, Zhang, and Berg, see Section 13.3 (Mosher *et
+al.* and references therein). mne_forward_solution approximates
+the solution with three dipoles in a homogeneous sphere whose locations
+and amplitudes are determined by minimizing the cost function:
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION and INLINE_EQUATION are
+the locations and amplitudes of the approximating dipoles and INLINE_EQUATION and INLINE_EQUATION are
+the potential distributions given by the true and approximative
+formulas, respectively. It can be shown that this integral can be
+expressed in closed form using an expansion of the potentials in
+spherical harmonics. The formula is evaluated for the most superficial
+dipoles, *i.e.*, those lying just inside the
+inner skull surface.
+
+.. _BJEFEJJG:
+
+Field derivatives
+=================
+
+If the --grad option is specified, mne_forward_solution includes
+the derivatives of the forward solution with respect to the dipole
+location coordinates to the output file. Let
+
+.. math:: 1 + 1 = 2
+
+be the INLINE_EQUATION matrix containing
+the signals produced by three orthogonal dipoles at location INLINE_EQUATION making
+up INLINE_EQUATIONthe gain matrix
+
+.. math:: 1 + 1 = 2
+
+With the --grad option, the output from mne_forward_solution also
+contains the INLINE_EQUATION derivative matrix
+
+.. math:: 1 + 1 = 2
+
+where
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION are the location
+coordinates of the INLINE_EQUATION dipole. If
+the dipole orientations are to the cortical normal with the --fixed
+option, the dimensions of INLINE_EQUATION and INLINE_EQUATION are INLINE_EQUATION and INLINE_EQUATION,
+respectively. Both INLINE_EQUATION and INLINE_EQUATION can
+be read with the mne_read_forward_solution Matlab
+function, see Table 10.1.
+
+.. _CHDBBFCA:
+
+Averaging forward solutions
+###########################
+
+Purpose
+=======
+
+One possibility to make a grand average over several runs
+of a experiment is to average the data across runs and average the
+forward solutions accordingly. For this purpose, mne_average_forward_solutions computes a
+weighted average of several forward solutions. The program averages both
+MEG and EEG forward solutions. Usually the EEG forward solution is
+identical across runs because the electrode locations do not change.
+
+Command line options
+====================
+
+mne_average_forward_solutions accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---fwd <name> :[<weight> ]**
+
+ Specifies a forward solution to include. If no weight is specified,
+ 1.0 is asssumed. In the averaging process the weights are divided
+ by their sum. For example, if two forward solutions are averaged
+ and their spefied weights are 2 and 3, the average is formed with
+ a weight of 2/5 for the first solution and 3/5 for the second one.
+
+**\---out <name>**
+
+ Specifies the output file which will contain the averaged forward solution.
diff --git a/doc/source/manual/index.rst b/doc/source/manual/index.rst
new file mode 100644
index 0000000..d0c3498
--- /dev/null
+++ b/doc/source/manual/index.rst
@@ -0,0 +1,23 @@
+==========
+MNE Manual
+==========
+
+.. toctree::
+ :maxdepth: 2
+
+ intro
+ list
+ cookbook
+ browse
+ forward
+ mne
+ analyse
+ morph
+ convert
+ matlab
+ utilities
+ sampledata
+ reading
+
+* :ref:`search`
+
diff --git a/doc/source/manual/intro.rst b/doc/source/manual/intro.rst
new file mode 100644
index 0000000..f81e389
--- /dev/null
+++ b/doc/source/manual/intro.rst
@@ -0,0 +1,45 @@
+
+
+.. _CHDDEFAB:
+
+============
+Introduction
+============
+
+This document describes a set of programs for preprocessing
+and averaging of MEG and EEG data and for constructing cortically-constrained minimum-norm
+estimates. This software package will in the sequel referred to
+as *MNE software*. The software is based on anatomical
+MRI processing, forward modelling, and source estimation methods published in
+Dale, Fischl, Hämäläinen, and others.
+The software depends on anatomical MRI processing tools provided
+by the FreeSurfer software.
+
+Chapter 2 of this manual gives an overview of the software
+modules included with MNE software. Chapter 3 is a concise cookbook
+describing a typical workflow for a novice user employing the convenience
+scripts as far as possible. Chapters 4 to 11 give more detailed
+information about the software modules. Chapter 12 discusses
+processing of the sample data set included with the MNE software. Chapter 13 lists
+some useful background material for the methods employed in the
+MNE software.
+
+Appendix A is an overview of the BEM model mesh
+generation methods, Appendix B contains information specific
+to the setup at Martinos Center of Biomedical Imaging, Appendix C is
+a software installation and configuration guide, Appendix D summarizes
+the software history, and Appendix E contains the End-User
+License Agreement.
+
+.. note:: The most recent version of this manual is available at ``$MNE_ROOT/share/doc/MNE-manual-`` <version> ``.pdf`` . For the present manual, <version> = ``2.7`` . For definition of the ``MNE_ROOT`` environment variable, see Section 2.4.
+
+We want to thank all MNE Software users at the Martinos Center and
+in other institutions for their collaboration during the creation
+of this software as well as for useful comments on the software
+and its documentation.
+
+The development of this software has been supported by the
+NCRR *Center for Functional Neuroimaging Technologies* P41RR14075-06, the
+NIH grants 1R01EB009048-01, R01 EB006385-A101, 1R01 HD40712-A1, 1R01
+NS44319-01, and 2R01 NS37462-05, ell as by Department of Energy
+under Award Number DE-FG02-99ER62764 to The MIND Institute.
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
new file mode 100644
index 0000000..ae173c0
--- /dev/null
+++ b/doc/source/manual/list.rst
@@ -0,0 +1,220 @@
+
+
+.. _CHDBAFGJ:
+
+========
+Overview
+========
+
+List of components
+##################
+
+The principal components of the MNE Software and their functions
+are listed in :ref:`CHDDJIDB`. Documented software is listed
+in italics. :ref:`BABDJHGH` lists various supplementary utilities.
+
+.. _CHDDJIDB:
+
+.. table:: The software components.
+
+ ============================ ============================================================================================================================================================================================================================================================================================
+ Name Purpose
+ ============================ ============================================================================================================================================================================================================================================================================================
+ *mne_analyze* An interactive analysis tool for computing source estimates, see Chapter 7.
+ *mne_average_estimates* Average data across subjects, see Section 8.6.2.
+ *mne_browse_raw* Interactive raw data browser. Includes filtering, offline averaging, and computation of covariance matrices, see Chapter 4.
+ *mne_compute_mne* Computes the minimum-norm estimates, see Section B.3.1. Most of the functionality of mne_compute_mne is included in mne_make_movie .
+ *mne_compute_raw_inverse* Compute the inverse solution from raw data, see Section 6.6.
+ *mne_convert_mne_data* Convert MNE data files to other file formats, see Section 9.12.
+ *mne_do_forward_solution* Convenience script to calculate the forward solution matrix, see Section 3.11.
+ *mne_do_inverse_operator* Convenience script to compute the inverse operator decomposition, see Section 3.13.
+ *mne_forward_solution* Calculate the forward solution matrix, see Section 5.9.
+ mne_inverse_operator Compute the inverse operator decomposition, see Section 6.4.
+ *mne_make_movie* Make movies in batch mode, see Section 6.5.
+ *mne_make_source_space* Create a *fif* source space description file, see Section 5.4.
+ *mne_process_raw* A batch-mode version of mne_browse_raw , see Chapter 4.
+ mne_redo_file Many intermediate result files contain a description of their 'production environment'. Such files can be recreated easily with this utility. This is convenient if, for example, the selection of bad channels is changed and the inverse operator decomposition has to be recalculated.
+ mne_redo_file_nocwd Works like mne_redo_file but does not try to change in to the working directory specified in the 'production environment'
+ *mne_setup_forward_model* Set up the BEM-related fif files, see Section 3.7.
+ *mne_setup_mri* A convenience script to create the fif files describing the anatomical MRI data, see Section 3.4.
+ *mne_setup_source_space* A convenience script to create a source space description file, see Section 3.5.
+ mne_show_environment Show information about the production environment of a file.
+ ============================ ============================================================================================================================================================================================================================================================================================
+
+.. _BABDJHGH:
+
+.. table:: Utility programs.
+
+ ================================== =========================================================================================================================================================================================
+ Name Purpose
+ ================================== =========================================================================================================================================================================================
+ *mne_add_patch_info* Add neighborhood information to a source space file, see Section 11.7.
+ mne_add_to_meas_info Utility to add new information to the measurement info block of a fif file. The source of information is another fif file.
+ mne_add_triggers Modify the trigger channel STI 014 in a raw data file, see Section 11.4.6. The same effect can be reached by using an event file for averaging in mne_process_raw and mne_browse_raw .
+ mne_annot2labels Convert parcellation data into label files, see Section 11.14.
+ *mne_anonymize* Remove subject-specific information from a fif data file, see Section 11.4.7.
+ *mne_average_forward_solutions* Calculate an average of forward solutions, see Section 5.10.
+ *mne_brain_vision2fiff* Convert EEG data from BrainVision format to fif format, see Section 9.2.10.
+ *mne_change_baselines* Change the dc offsets according to specifications given in a text file, see Section 11.12.
+ mne_change_nave Change the number of averages in an evoked-response data file. This is often necessary if the file was derived from several files.
+ *mne_check_eeg_locations* Checks that the EEG electrode locations have been correctly transferred from the Polhemus data block to the channel information tags, see Section 11.4.3.
+ mne_check_surface Check the validity of a FreeSurfer surface file or one of the surfaces within a BEM file. This program simply checks for topological errors in surface files.
+ mne_collect_transforms Collect coordinate transformations from several sources into a single fif file, see Section 9.9.
+ mne_compensate_data Change the applied software gradient compensation in an evoked-response data file, see Section 9.2.4.
+ *mne_convert_lspcov* Convert the LISP format noise covariance matrix output by graph into fif, see Section 9.11.
+ *mne_convert_ncov* Convert the ncov format noise covariance file to fif, see Section 9.10.
+ *mne_convert_surface* Convert FreeSurfer and text format surface files into Matlab mat files, see Section 9.7.
+ *mne_cov2proj* Pick eigenvectors from a covariance matrix and create a signal-space projection (SSP) file out of them, see Section 11.9.
+ mne_create_comp_data Create a fif file containing software gradient compensation information from a text file, see Section 9.2.6.
+ *mne_ctf2fiff* Convert a CTF ds folder into a fif file, see Section 9.2.2.
+ mne_ctf_dig2fiff Convert text format digitization data to fif format, see Section 9.2.3.
+ mne_dicom_essentials List essential information from a DICOM file. This utility is used by the script mne_organize_dicom, see Section A.2.1.
+ mne_edf2fiff Convert EEG data from the EDF/EDF+/BDF formats to the fif format, see Section 9.2.8.
+ mne_epochs2mat Apply bandpass filter to raw data and extract epochs for subsequent processing in Matlab, see Section 9.14.
+ mne_evoked_data_summary List summary of averaged data from a fif file to the standard output.
+ *mne_eximia2fiff* Convert EEG data from the Nexstim eXimia system to fif format, see Section 9.2.11.
+ *mne_fit_sphere_to_surf* Fit a sphere to a surface given in either fif or FreeSurfer format, see Section 11.9.
+ *mne_fix_mag_coil_types* Update the coil types for magnetometers in a fif file, see Section 11.4.4.
+ *mne_fix_stim14* Fix coding errors of trigger channel STI 014, see Section 3.9.1.
+ mne_flash_bem Create BEM tessellation using multi-echo FLASH MRI data, see Section A.2.
+ mne_insert_4D_comp Read Magnes compensation channel data from a text file and merge it with raw data from other channels in a fif file, see Section 9.2.5
+ *mne_list_bem* List BEM information in text format, see Section 9.6.
+ *mne_list_coil_def* Create the coil description file. This is run automatically at when the software is set up, see Section 5.8.5.
+ mne_list_proj List signal-space projection data from a fif file.
+ *mne_list_source_space* List source space information in text format suitable for importing into Neuromag MRIlab software, see Section 9.5.
+ *mne_list_versions* List versions and compilation dates of MNE software modules, see Section 11.2.
+ *mne_make_cor_set* Used by mne_setup_mri to create fif format MRI description files from COR or mgh/mgz format MRI data, see Section 3.4. The mne_make_cor_set utility is described in Section 9.8.
+ mne_make_derivations Create a channel derivation data file, see Section 11.5.
+ *mne_make_eeg_layout* Make a topographical trace layout file using the EEG electrode locations from an actual measurement, see Section 11.6.
+ *mne_make_morph_maps* Precompute the mapping data needed for morphing between subjects, see Section 8.4.
+ mne_make_uniform_stc Create a spatially uniform stc file for testing purposes.
+ *mne_mark_bad_channels* Update the list of unusable channels in a data file, see Section 11.4.1.
+ *mne_morph_labels* Morph label file definitions between subjects, see Section 8.5.
+ mne_organize_dicom Organized DICOM MRI image files into directories, see Section A.2.1.
+ *mne_prepare_bem_model* Perform the geometry calculations for BEM forward solutions, see Section 5.7.
+ mne_process_stc Manipulate stc files.
+ *mne_raw2mat* Convert raw data into a Matlab file, see Section 9.13.
+ *mne_rename_channels* Change the names and types of channels in a fif file, see Section 11.4.5.
+ *mne_sensitivity_map* Compute a sensitivity map and output the result in a w-file, see Section 11.10.
+ mne_sensor_locations Create a file containing the sensor locations in text format.
+ mne_show_fiff List contents of a fif file, see Section 11.3
+ *mne_simu* Simulate MEG and EEG data, see Section 11.13.
+ *mne_smooth* Smooth a w or stc file.
+ *mne_surf2bem* Create a *fif* file describing the triangulated compartment boundaries for the boundary-element model (BEM), see Section 5.6.
+ mne_toggle_skips Change data skip tags in a raw file into ignored skips or vice versa.
+ *mne_transform_points* Transform between MRI and MEG head coordinate frames, see Section 11.11.
+ *mne_tufts2fiff* Convert EEG data from the Tufts University format to fif format, see Section 9.2.9.
+ mne_view_manual Starts a PDF reader to show this manual from its standard location.
+ *mne_volume_data2mri* Convert volumetric data defined in a source space created with mne_volume_source_space into an MRI overlay, see Section 9.4.
+ *mne_volume_source_space* Make a volumetric source space, see Section 5.5.
+ *mne_watershed_bem* Do the segmentation for BEM using the watershed algorithm, see Section A.1.
+ ================================== =========================================================================================================================================================================================
+
+File formats
+############
+
+The MNE software employs the fif file format whenever possible.
+New tags have been added to incorporate information specific to
+the calculation of cortically contained source estimates. FreeSurfer
+file formats are also employed when needed to represent cortical
+surface geometry data as well as spatiotemporal distribution of
+quantities on the surfaces. Of particular interest are the w files,
+which contain static overlay data on the cortical surface and stc files,
+which contain dynamic overlays (movies).
+
+Conventions
+###########
+
+When command line examples are shown, the backslash character
+(\\) indicates a continuation line. It is also valid in the shells.
+In most cases, however, you can easily fit the commands listed in
+this manual on one line and thus omit the backslashes. The order
+of options is irrelevant. Entries to be typed literally are shown
+like ``this`` . *Italicized* text indicates
+conceptual entries. For example, *<dir>* indicates a directory
+name.
+
+In the description of interactive software modules the notation <menu>/<item> is
+often used to denotes menu selections. For example, File/Quit stands
+for the Quit button in the File menu.
+
+All software modules employ the double-dash (--) option convention, *i.e.*, the
+option names are preceded by two dashes.
+
+Most of the programs have two common options to obtain general
+information:
+
+**\---help**
+
+ Prints concise usage information.
+
+**\---version**
+
+ Prints the program module name, version number, and compilation date.
+
+.. _CIHCDHGI:
+
+User environment
+################
+
+The system-dependent location of the MNE Software will be
+here referred to by the environment variable MNE_ROOT. There are
+two scripts for setting up user environment so that the software
+can be used conveniently:
+
+``$MNE_ROOT/bin/mne_setup_sh``
+
+and
+
+``$MNE_ROOT/bin/mne_setup``
+
+compatible with the POSIX and csh/tcsh shells, respectively. Since
+the scripts set environment variables they should be 'sourced' to
+the present shell. You can find which type of a shell you are using
+by saying
+
+``echo $SHELL``
+
+If the output indicates a POSIX shell (bash or sh) you should issue
+the three commands:
+
+``export MNE_ROOT=`` <MNE> ``export MATLAB_ROOT=`` <Matlab> ``. $MNE_ROOT/bin/mne_setup_sh``
+
+with <MNE> replaced
+by the directory where you have installed the MNE software and <Matlab> is
+the directory where Matlab is installed. If you do not have Matlab,
+leave MATLAB_ROOT undefined. If Matlab is not available, the utilities mne_convert_mne_data , mne_epochs2mat , mne_raw2mat ,
+and mne_simu will not work.
+
+For csh/tcsh the corresponding commands are:
+
+``setenv MNE_ROOT`` <MNE> ``setenv MATLAB_ROOT`` <Matlab> ``source $MNE_ROOT/bin/mne_setup``
+
+For BEM mesh generation using the watershed algorithm or
+on the basis of multi-echo FLASH MRI data (see Appendix A) and
+for accessing the tkmedit program
+from mne_analyze , see Section 7.18,
+the MNE software needs access to a FreeSurfer license
+and software. Therefore, to use these features it is mandatory that
+you set up the FreeSurfer environment
+as described in the FreeSurfer documentation.
+
+The environment variables relevant to the MNE software are
+listed in :ref:`CIHDGFAA`
+
+.. _CIHDGFAA:
+
+.. table:: Environment variables
+
+ ====================== =============================================================================================================================================================
+ Name of the variable Description
+ ====================== =============================================================================================================================================================
+ MNE_ROOT Location of the MNE software, see above
+ FREESURFER_HOME Location of the FreeSurfer software. Needed during FreeSurfer reconstruction and if the FreeSurfer MRI viewer is used with mne_analyze , see Section 7.18.
+ SUBJECTS_DIR Location of the MRI data
+ SUBJECT Name of the current subject
+ MNE_TRIGGER_CH_NAME Name of the trigger channel in raw data, see Section 4.2.1.
+ MNE_TRIGGER_CH_MASK Mask to be applied to the trigger channel values, see Section 4.2.1.
+ ====================== =============================================================================================================================================================
+
+.. note:: Appendix B contains information specific to the setup at the Martinos Center including instructions to access the Neuromag software.
diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst
new file mode 100644
index 0000000..f69f991
--- /dev/null
+++ b/doc/source/manual/matlab.rst
@@ -0,0 +1,714 @@
+
+
+.. _CHDBFDFG:
+
+==================
+The Matlab toolbox
+==================
+
+Overview
+########
+
+The MNE software contains a collection Matlab m-files to
+facilitate interfacing with binary file formats of the MNE software.
+The toolbox is located at ``$MNE_ROOT/share/matlab`` . The
+names of the MNE Matlab toolbox functions begin either with mne_ or
+with fiff_ . When you source the mne_setup script
+as described in Section 2.4 on of the following actions
+takes place:
+
+- If you do not have the Matlab startup.m
+ file, it will be created and lines allowing access to the MNE Matlab
+ toolbox are added.
+
+- If you have startup.m and it does not have the standard MNE
+ Matlab toolbox setup lines, you will be instructed to add them manually.
+
+- If you have startup.m and the standard MNE Matlab toolbox
+ setup lines are there, nothing happens.
+
+A summary of the available routines is provided in Tables :ref:`BGBCGHAG` - :ref:`BGBEFADJ`. The toolbox
+also contains a set of examples which may be usedful starting points
+for your own development. The names of these functions startwith mne_ex and
+they are listed in :ref:`BGBEFADJ`.
+
+.. note:: The MNE Matlab Toolbox is compatible with Matlab versions 7.0 or later.
+
+.. note:: The matlab function fiff_setup_read_raw has a significant change. The sample numbers now take into account possible initial skip in the file, *i.e.*, the time between the start of the data acquisition and the start of saving the data to disk. The first_samp member of the returned structure indicates the initial skip in samples. If you want your own routines, which assume that initial skip has been removed, perform identically with the previous version, subt [...]
+
+.. _BGBCGHAG:
+
+.. table:: High-level reading routines.
+
+ ============================== ===========================================================================================
+ Function Purpose
+ ============================== ===========================================================================================
+ fiff_find_evoked Find all evoked data sets from a file.
+ fiff_read_bad_channels Read the bad channel list.
+ fiff_read_ctf_comp Read CTF software gradient compensation data.
+ fiff_read_evoked Read evoked-response data.
+ fiff_read_evoked_all Read all evoked-response data from a file.
+ fiff_read_meas_info Read measurement information.
+ fiff_read_mri Read an MRI description file.
+ fiff_read_proj Read signal-space projection data.
+ fiff_read_raw_segment Read a segment of raw data with time limits are specified in samples.
+ fiff_read_raw_segment_times Read a segment of raw data with time limits specified in seconds.
+ fiff_setup_read_raw Set up data structures before using fiff_read_raw_segment or fiff_read_raw_segment_times
+ ============================== ===========================================================================================
+
+.. table:: Channel selection utilities.
+
+ ============================ ==================================================================================================================================================
+ Function Purpose
+ ============================ ==================================================================================================================================================
+ fiff_pick_channels Create a selector to pick desired channels from data according to include and exclude lists.
+ fiff_pick_channels_evoked Pick desired channels from evoked-response data according to include and exclude lists
+ fiff_pick_info Modify measurement info to include only selected channels.
+ fiff_pick_types Create a selector to pick desired channels from data according to channel types (MEG, EEG, STIM) in combination with include and exclude lists.
+ fiff_pick_types_evoked Pick desired channels from evoked-response data according to channel types (MEG, EEG, STIM) in combination with include and exclude lists.
+ ============================ ==================================================================================================================================================
+
+.. table:: Coordinate transformation utilities.
+
+ ========================= =============================================================================================================================
+ Function Purpose
+ ========================= =============================================================================================================================
+ fiff_invert_transform Invert a coordinate transformation structure.
+ fiff_reset_ch_pos Reset channel position transformation to the default values present in the file.
+ fiff_transform_eeg_chs Transform electrode positions to another coordinate frame.
+ fiff_transform_meg_chs Apply a coordinate transformation to the sensor location data to bring the integration points to another coordinate frame.
+ ========================= =============================================================================================================================
+
+.. table:: Basic reading routines.
+
+ ========================= ========================================================================
+ Function Purpose
+ ========================= ========================================================================
+ fiff_define_constants Define a structure which contains the constant relevant to fif files.
+ fiff_dir_tree_find Find nodes of a given type in a directory tree structure.
+ fiff_list_dir_tree List a directory tree structure.
+ fiff_make_dir_tree Create a directory tree structure.
+ fiff_open Open a fif file and create the directory tree structure.
+ fiff_read_named_matrix Read a named matrix from a fif file.
+ fiff_read_tag Read one tag from a fif file.
+ fiff_read_tag_info Read the info of one tag from a fif file.
+ fiff_split_name_list Split a colon-separated list of names into a cell array of strings.
+ ========================= ========================================================================
+
+.. table:: Writing routines.
+
+ =================================== ===============================================
+ Function Purpose
+ =================================== ===============================================
+ fiff_end_block Write a FIFF_END_BLOCK tag.
+ fiff_end_file Write the standard closing.
+ fiff_start_block Write a FIFF_START_BLOCK tag.
+ fiff_start_file Write the appropriate beginning of a file.
+ fiff_write_ch_info Write a channel information structure.
+ fiff_write_coord_trans Write a coordinate transformation structure.
+ fiff_write_ctf_comp Write CTF compensation data.
+ fiff_write_dig_point Write one digitizer data point.
+ fiff_write_complex Write single-precision complex numbers.
+ fiff_write_complex_matrix Write a single-precision complex matrix.
+ fiff_write_double Write double-precision floats.
+ fiff_write_double_complex Write double-precision complex numbers.
+ fiff_write_double_complex_matrix Write a double-precision complex matrix
+ fiff_write_double_matrix Write a double-precision matrix
+ fiff_write_evoked Write an evoked-reponse data file.
+ fiff_write_float Write single-precision floats.
+ fiff_write_float_matrix Write a single-precision matrix.
+ fiff_write_id Write an id tag.
+ fiff_write_int Write 32-bit integers.
+ fiff_write_int_matrix Write a matrix of 32-bit integers.
+ fiff_write_name_list Write a name list.
+ fiff_write_named_matrix Write a named matrix.
+ fiff_write_proj Write SSP data.
+ fiff_write_short Write 16-bit integers.
+ fiff_write_string Write a string.
+ =================================== ===============================================
+
+.. table:: High-level data writing routines.
+
+ ========================== ==================================================================================
+ Function Purpose
+ ========================== ==================================================================================
+ fiff_write_evoked Write an evoked-response data file.
+ fiff_finish_writing_raw Write the closing tags to a raw data file.
+ fiff_start_writing_raw Start writing raw data file, *i.e.*, write the measurement information.
+ fiff_write_dig_file Write a fif file containing digitization data.
+ fiff_write_raw_buffer Write one raw data buffer. This is used after a call to fiff_start_writing_raw.
+ ========================== ==================================================================================
+
+.. table:: Coil definition utilities.
+
+ ==================== ======================================================================
+ Function Purpose
+ ==================== ======================================================================
+ mne_add_coil_defs Add coil definitions to an array of channel information structures.
+ mne_load_coil_def Load a coil definition file.
+ ==================== ======================================================================
+
+.. table:: Routines for software gradient compensation and signal-space projection.
+
+ ========================== ==================================================================================================================================================
+ Function Purpose
+ ========================== ==================================================================================================================================================
+ mne_compensate_to Apply or remove CTF software gradient compensation from evoked-response data.
+ mne_get_current_comp Get the state of software gradient compensation from measurement info.
+ mne_make_compensator Make a compensation matrix which switches the status of CTF software gradient compensation from one state to another.
+ mne_make_projector Create a signal-space projection operator with the projection item definitions and cell arrays of channel names and bad channel names as input.
+ mne_make_projector_info Like mne_make_projector but uses the measurement info structure as input.
+ mne_set_current_comp Change the information about the compensation status in measurement info.
+ ========================== ==================================================================================================================================================
+
+.. table:: High-level routines for reading MNE data files.
+
+ ============================ =====================================================================================
+ Function Purpose
+ ============================ =====================================================================================
+ mne_pick_channels_cov Pick desired channels from a sensor covariance matrix.
+ mne_pick_channels_forward Pick desired channels (rows) from a forward solution.
+ mne_read_bem_surfaces Read triangular tessellations of surfaces for boundary-element models
+ mne_read_cov Read a covariance matrix.
+ mne_read_epoch Read an epoch of data from the output file of mne_epochs2mat .
+ mne_read_events Read an event list from a fif file produced by mne_browse_raw or mne_process_raw .
+ mne_read_forward_solution Read a forward solution from a fif file.
+ mne_read_inverse_operator Read an inverse operator from a fif file.
+ mne_read_morph_map Read an morphing map produced with mne_make_morph_maps , see Section 8.4.
+ mne_read_noise_cov Read a noise-covariance matrix from a fif file.
+ mne_read_source_spaces Read source space information from a fif file.
+ ============================ =====================================================================================
+
+.. table:: High-level routines for writing MNE data files.
+
+ ============================ ================================================================================================
+ Function Purpose
+ ============================ ================================================================================================
+ mne_write_cov Write a covariance matrix to an open file.
+ mne_write_cov_file Write a complete file containing just a covariance matrix.
+ mne_write_events Write a fif format event file compatible with mne_browse_raw and mne_process_raw .
+ mne_write_inverse_sol_stc Write stc files containing an inverse solution or other dynamic data on the cortical surface.
+ mne_write_inverse_sol_w Write w files containing an inverse solution or other static data on the cortical surface
+ ============================ ================================================================================================
+
+.. _BABBDDAI:
+
+.. table:: Routines related to stc, w, and label files.
+
+ ========================= ==========================================================================================================================================
+ Function Purpose
+ ========================= ==========================================================================================================================================
+ mne_read_stc_file Read data from one stc file. The vertex numbering in the returned structure will start from 0.
+ mne_read_stc_file1 Read data from one stc file. The vertex numbering in the returned structure will start from 1.
+ mne_read_w_file Read data from one w file. The vertex numbering in the returned structure will start from 0.
+ mne_read_w_file1 Read data from one w file. The vertex numbering in the returned structure will start from 1.
+ mne_write_stc_file Write a new stc file. It is assumed the the vertex numbering in the input data structure containing the stc information starts from 0.
+ mne_write_stc_file1 Write a new stc file. It is assumed the the vertex numbering in the input data structure containing the stc information starts from 1.
+ mne_write_w_file Write a new w file. It is assumed the the vertex numbering in the input data structure containing the w file information starts from 0.
+ mne_write_w_file1 Write a new w file. It is assumed the the vertex numbering in the input data structure containing the w file information starts from 1.
+ mne_read_label_file Read a label file (ROI)
+ mne_write_label_file Write a label file (ROI)
+ mne_label_time_courses Extract time courses corresponding to a label from an stc file.
+ ========================= ==========================================================================================================================================
+
+.. table:: Routines for reading FreeSurfer surfaces.
+
+ ===================== ==============================================================================================================================
+ Function Purpose
+ ===================== ==============================================================================================================================
+ mne_read_curvature Read a curvature file.
+ mne_read_surface Read one surface, return the vertex locations and triangulation info.
+ mne_read_surfaces Read surfaces corresponding to one or both hemispheres. Optionally read curvature information and add derived surface data.
+ mne_reduce_surface Reduce the number of triangles on a surface using the reducepatch Matlab function.
+ mne_write_surface Write a FreeSurfer surface file.
+ ===================== ==============================================================================================================================
+
+.. _BGBEGFBD:
+
+.. table:: Utility functions.
+
+ ================================ ==============================================================================================================================================================
+ Function Purpose
+ ================================ ==============================================================================================================================================================
+ mne_block_diag Create a sparse block-diagonal matrix out of a vector.
+ mne_combine_xyz Calculate the square sum of the three Cartesian components of several vectors listed in one row or column vector.
+ mne_file_name Compose a file name relative to $MNE_ROOT
+ mne_find_channel Find a channel by name from measurement info.
+ mne_find_source_space_hemi Determine whether a given source space belongs to the left or right hemisphere.
+ mne_fread3 Read a three-byte integer.
+ mne_fwrite3 Write a three-byte integer.
+ mne_make_combined_event_file Combine data from several trigger channels into one event file.
+ mne_omit_first_line Omit first line from a multi-line message. This routine is useful for formatting error messages.
+ mne_prepare_inverse_operator Prepare inverse operator data for calculating L2 minimum-norm solutions and dSPM.
+ mne_setup_toolbox Set up the MNE Matlab toolbox.
+ mne_transform_coordinates Transform locations between different coordinate systems. This function uses the output file from mne_collect_transforms described in Section 9.9 as input.
+ mne_transpose_named_matrix Create a transpose of a named matrix.
+ mne_transform_source_space_to Transform source space data to another coordinate frame.
+ ================================ ==============================================================================================================================================================
+
+.. _BGBEFADJ:
+
+.. table:: Examples demostrating the use of the toolbox.
+
+ ========================= =================================================================================
+ Function Purpose
+ ========================= =================================================================================
+ mne_ex_average_epochs Example of averaging epoch data produced by mne_epochs2mat , see Section 9.14.
+ mne_ex_cancel_noise Example of noise cancellation procedures.
+ mne_ex_compute_inverse Example of computing a L2 minimum-norm estimate or a dSPM solution
+ mne_ex_data_sets Example of listing evoked-response data sets.
+ mne_ex_evoked_grad_amp Compute tangential gradient amplitudes from planar gradiometer data.
+ mne_ex_read_epochs Read epoch data from a raw data file.
+ mne_ex_read_evoked Example of reading evoked-response data.
+ mne_ex_read_raw Example of reading raw data.
+ mne_ex_read_write_raw Example of processing raw data (read and write).
+ ========================= =================================================================================
+
+.. note:: In order for the inverse operator calculation to work correctly with data processed with the Elekta-Neuromag Maxfilter (TM) software, the so-called *processing history* block must be included in data files. Previous versions of the MNE Matlab functions did not copy processing history to files saved. As of March 30, 2009, the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enchanced to include these data to the output file as appr [...]
+
+Some data structures
+####################
+
+The MNE Matlab toolbox relies heavily on structures to organize
+the data. This section gives detailed information about fields in
+the essential data structures employed in the MNE Matlab toolbox.
+In the structure definitions, data types referring to other MNE
+Matlab toolbox structures are shown in italics. In addition, :ref:`BGBJHCGD` lists the values of various FIFF constants
+defined by fiff_define_constants.m .
+The documented structures are:
+
+**tag**
+
+ Contains one tag from the fif file, see :ref:`BGBGIIGD`.
+
+**taginfo**
+
+ Contains the information about one tag, see :ref:`BGBBJBJJ`.
+
+**directory**
+
+ Contains the tag directory as a tree structure, see :ref:`BGBEDHBG`.
+
+**id**
+
+ A fif ID, see :ref:`BGBDAHHJ`.
+
+**named matrix**
+
+ Contains a matrix with names for rows and/or columns, see :ref:`BGBBEDID`. A named matrix is used to store, *e.g.*,
+ SSP vectors and forward solutions.
+
+**trans**
+
+ A 4 x 4 coordinate-transformation matrix operating on augmented column
+ vectors. Indication of the coordinate frames to which this transformation
+ relates is included, see :ref:`BGBDHBIF`.
+
+**dig**
+
+ A Polhemus digitizer data point, see :ref:`BGBHDEDG`.
+
+**coildef**
+
+ The coil definition structure useful for forward calculations and array
+ visualization, see :ref:`BGBGBEBH`. For more detailed information on
+ coil definitions, see Section 5.8.
+
+**ch**
+
+ Channel information structure, see :ref:`BGBIABGD`.
+
+**proj**
+
+ Signal-space projection data, see :ref:`BGBCJHJB`.
+
+**comp**
+
+ Software gradiometer compensation data, see :ref:`BGBJDIFD`.
+
+**measurement info**
+
+ Translation of the FIFFB_MEAS_INFO entity, see :ref:`BGBFHDIJ`. This
+ data structure is returned by fiff_read_meas_info .
+
+**surf**
+
+ Used to represent triangulated surfaces and cortical source spaces, see :ref:`BGBEFJCB`.
+
+**cov**
+
+ Used for storing covariance matrices, see :ref:`BGBJJIED`.
+
+**fwd**
+
+ Forward solution data returned by mne_read_forward_solution ,
+ see :ref:`BGBFJIBJ`.
+
+**inv**
+
+ Inverse operator decomposition data returned by mne_read_inverse_operator ,
+ see :ref:`BGBIEIJE`. For more information on inverse operator
+ decomposition, see Section 6.2. For an example on how to
+ compute inverse solution using this data, see the sample routine mne_ex_compute_inverse .
+
+.. note:: The MNE Matlab toolbox tries it best to employ vertex numbering starting from 1 as opposed to 0 as recorded in the data files. There are, however, two exceptions where explicit attention to the vertex numbering convention is needed. First, the standard stc and w file reading and writing routines return and assume zero-based vertex numbering. There are now versions with names ending with '1' , which return and assume one-based vertex numbering, see :ref:`BAB [...]
+
+.. _BGBJHCGD:
+
+.. table:: FIFF constants.
+
+ ================================ ======= ======================================================================================================
+ Name Value Description
+ ================================ ======= ======================================================================================================
+ FIFFV_MEG_CH 1 This is a MEG channel.
+ FIFFV_REF_MEG_CH 301 This a reference MEG channel, located far away from the head.
+ FIFFV_EEF_CH 2 This is an EEG channel.
+ FIFFV_MCG_CH 201 This a MCG channel.
+ FIFFV_STIM_CH 3 This is a digital trigger channel.
+ FIFFV_EOG_CH 202 This is an EOG channel.
+ FIFFV_EMG_CH 302 This is an EMG channel.
+ FIFFV_ECG_CH 402 This is an ECG channel.
+ FIFFV_MISC_CH 502 This is a miscellaneous analog channel.
+ FIFFV_RESP_CH 602 This channel contains respiration monitor output.
+ FIFFV_COORD_UNKNOWN 0 Unknown coordinate frame
+ FIFFV_COORD_DEVICE 1 The MEG device coordinate frame
+ FIFFV_COORD_ISOTRAK 2 The Polhemus digitizer coordinate frame (does not appear in data files).
+ FIFFV_COORD_HPI 3 HPI coil coordinate frame (does not appear in data files)
+ FIFFV_COORD_HEAD 4 The MEG head coordinate frame (Neuromag convention).
+ FIFFV_COORD_MRI 5 The MRI coordinate frame
+ FIFFV_COORD_MRI_SLICE 6 The coordinate frame of a single MRI slice.
+ FIFFV_COORD_MRI_DISPLAY 7 The preferred coordinate frame for displaying the MRIs (used by MRIlab).
+ FIFFV_COORD_DICOM_DEVICE 8 The DICOM coordinate frame (does not appear in files).
+ FIFFV_COORD_IMAGING_DEVICE 9 A generic imaging device coordinate frame (does not appear in files).
+ FIFFV_MNE_COORD_TUFTS_EEG 300 The Tufts EEG data coordinate frame
+ FIFFV_MNE_COORD_CTF_DEVICE 1001 The CTF device coordinate frame (does not appear in files)
+ FIFFV_MNE_COORD_CTF_HEAD 1004 The CTF/4D head coordinate frame
+ FIFFV_ASPECT_AVERAGE 100 Data aspect: average.
+ FIFFV_ASPECT_STD_ERR 101 Data aspect: standard error of mean.
+ FIFFV_ASPECT_SINGLE 102 Single epoch.
+ FIFFV_ASPECT_SUBAVERAGE 103 One subaverage.
+ FIFFV_ASPECT_ALTAVERAGE 104 One alternating (plus-minus) subaverage.
+ FIFFV_ASPECT_SAMPLE 105 A sample cut from raw data.
+ FIFFV_ASPECT_POWER_DENSITY 106 Power density spectrum.
+ FIFFV_ASPECT_DIPOLE_WAVE 200 The time course of an equivalent current dipole
+ FIFFV_BEM_SURF_ID_UNKNOWN -1 Unknown BEM surface
+ FIFFV_BEM_SURF_ID_BRAIN 1 The inner skull surface
+ FIFFV_BEM_SURF_ID_SKULL 3 The outer skull surface
+ FIFFV_BEM_SURF_ID_HEAD 4 The scalp surface
+ FIFFV_MNE_SURF_LEFT_HEMI 101 Left hemisphere cortical surface
+ FIFFV_MNE_SURF_RIGHT_HEMI 102 Right hemisphere cortical surface
+ FIFFV_POINT_CARDINAL 1 Digitization point which is a cardinal landmark aka. fiducial point
+ FIFFV_POINT_HPI 2 Digitized HPI coil location
+ FIFFV_POINT_EEG 3 Digitized EEG electrode location
+ FIFFV_POINT_ECG 3 Digitized ECG electrode location
+ FIFFV_POINT_EXTRA 4 Additional head surface point
+ FIFFV_POINT_LPA 1 Identifier for left auricular landmark
+ FIFFV_POINT_NASION 2 Identifier for nasion
+ FIFFV_POINT_RPA 3 Identifier for right auricular landmark
+ FIFFV_MNE_FIXED_ORI 1 Fixed orientation constraint used in the computation of a forward solution.
+ FIFFV_MNE_FREE_ORI 2 No orientation constraint used in the computation of a forward solution
+ FIFFV_MNE_MEG 1 Indicates an inverse operator based on MEG only
+ FIFFV_MNE_EEG 2 Indicates an inverse operator based on EEG only.
+ FIFFV_MNE_MEG_EEG 3 Indicates an inverse operator based on both MEG and EEG.
+ FIFFV_MNE_UNKNOWN_COV 0 An unknown covariance matrix
+ FIFFV_MNE_NOISE_COV 1 Indicates a noise covariance matrix.
+ FIFFV_MNE_SENSOR_COV 1 Synonym for FIFFV_MNE_NOISE_COV
+ FIFFV_MNE_SOURCE_COV 2 Indicates a source covariance matrix
+ FIFFV_MNE_FMRI_PRIOR_COV 3 Indicates a covariance matrix associated with fMRI priors
+ FIFFV_MNE_SIGNAL_COV 4 Indicates the data (signal + noise) covariance matrix
+ FIFFV_MNE_DEPTH_PRIOR_COV 5 Indicates the depth prior (depth weighting) covariance matrix
+ FIFFV_MNE_ORIENT_PRIOR_COV 6 Indicates the orientation (loose orientation constrain) prior covariance matrix
+ FIFFV_PROJ_ITEM_NONE 0 The nature of this projection item is unknown
+ FIFFV_PROJ_ITEM_FIELD 1 This is projection item is a generic field pattern or field patters.
+ FIFFV_PROJ_ITEM_DIP_FIX 2 This projection item is the field of one dipole
+ FIFFV_PROJ_ITEM_DIP_ROT 3 This projection item corresponds to the fields of three or two orthogonal dipoles at some location.
+ FIFFV_PROJ_ITEM_HOMOG_GRAD 4 This projection item contains the homogeneous gradient fields as seen by the sensor array.
+ FIFFV_PROJ_ITEM_HOMOG_FIELD 5 This projection item contains the three homogeneous field components as seen by the sensor array.
+ FIFFV_MNE_PROJ_ITEM_EEG_AVREF 10 This projection item corresponds to the average EEG reference.
+ ================================ ======= ======================================================================================================
+
+.. _BGBGIIGD:
+
+.. table:: The tag structure.
+
+ ======= =========== ============================================
+ Field Data type Description
+ ======= =========== ============================================
+ kind int32 The kind of the data item.
+ type uint32 The data type used to represent the data.
+ size int32 Size of the data in bytes.
+ next int32 Byte offset of the next tag in the file.
+ data various The data itself.
+ ======= =========== ============================================
+
+.. _BGBBJBJJ:
+
+.. table:: The taginfo structure.
+
+ ======= =========== ============================================
+ Field Data type Description
+ ======= =========== ============================================
+ kind double The kind of the data item.
+ type double The data type used to represent the data.
+ size double Size of the data in bytes.
+ pos double Byte offset to this tag in the file.
+ ======= =========== ============================================
+
+.. _BGBEDHBG:
+
+.. table:: The directory structure.
+
+ ============ ============ ================================================================
+ Field Data type Description
+ ============ ============ ================================================================
+ block double The block id of this directory node.
+ id id The unique identifier of this node.
+ parent_id id The unique identifier of the node this node was derived from.
+ nent double Number of entries in this node.
+ nchild double Number of children to this node.
+ dir taginfo Information about tags in this node.
+ children directory The children of this node.
+ ============ ============ ================================================================
+
+.. _BGBDAHHJ:
+
+.. table:: The id structure.
+
+ ========== =========== ============================================================
+ Field Data type Description
+ ========== =========== ============================================================
+ version int32 The fif file version (major << 16 | minor).
+ machid int32(2) Unique identifier of the computer this id was created on.
+ secs int32 Time since January 1, 1970 (seconds).
+ usecs int32 Time since January 1, 1970 (microseconds past secs ).
+ ========== =========== ============================================================
+
+.. _BGBBEDID:
+
+.. table:: The named matrix structure.
+
+ ============ =========== ======================================================================
+ Field Data type Description
+ ============ =========== ======================================================================
+ nrow int32 Number of rows.
+ ncol int32 Number of columns.
+ row_names cell\ The names of associated with the rows. This member may be empty.
+ col_names cell\ The names of associated with the columns. This member may be empty.
+ data various The matrix data, usually of type single or double.
+ ============ =========== ======================================================================
+
+.. _BGBDHBIF:
+
+.. table:: The trans structure.
+
+ ======== ============== =====================================================================================================================================================================
+ Field Data type Description
+ ======== ============== =====================================================================================================================================================================
+ from int32 The source coordinate frame, see :ref:`BGBJHCGD`. Look for entries starting with FIFFV_COORD or FIFFV_MNE_COORD.
+ to int32 The destination coordinate frame.
+ trans double(4,4) The 4-by-4 coordinate transformation matrix. This operates from augmented position column vectors given in *from* coordinates to give results in *to* coordinates.
+ ======== ============== =====================================================================================================================================================================
+
+.. _BGBHDEDG:
+
+.. table:: The dig structure.
+
+ ======== ============ ==========================================================================================================================
+ Field Data type Description
+ ======== ============ ==========================================================================================================================
+ kind int32 The type of digitizing point. Possible values are listed in :ref:`BGBJHCGD`. Look for entries starting with FIFF_POINT.
+ ident int32 Identifier for this point.
+ r single(3) The location of this point.
+ ======== ============ ==========================================================================================================================
+
+.. _BGBGBEBH:
+
+.. table:: The coildef structure. For more detailed information, see Section 5.8.
+
+ ============== ======================= ========================================================================================
+ Field Data type Description
+ ============== ======================= ========================================================================================
+ class double The coil (or electrode) class
+ id double The coil (or electrode) id
+ accuracy double Representation accuracy
+ num_points double Number of integration points.
+ size double Coil size
+ baseline double Coil baseline
+ description char\ Coil description
+ coildefs double(num_points,7) Each row contains the integration point weight, followed by location\] and normal
+ FV struct Contains the faces and vertices which can be used to draw the coil for visualization.
+ ============== ======================= ========================================================================================
+
+.. _BGBIABGD:
+
+.. table:: The ch structure.
+
+ ============== ============== =======================================================================================================================================================================================================================================================================================================================================================
+ Field Data type Description
+ ============== ============== =======================================================================================================================================================================================================================================================================================================================================================
+ scanno int32 Scanning order number, starting from 1.
+ logno int32 Logical channel number, conventions in the usage of this number vary.
+ kind int32 The channel type (FIFFV_MEG_CH, FIFF_EEG_CH, etc., see :ref:`BGBJHCGD` ).
+ range double The hardware-oriented part of the calibration factor. This should be only applied to the continuous raw data.
+ cal double The calibration factor to bring the channels to physical units.
+ loc double(12) The channel location. The first three numbers indicate the location\], followed by the three unit vectors of the channel-specific coordinate frame. These data contain the values saved in the fif file and should not be changed. The values are specified in device coordinates for MEG and in head coordinates for EEG channels, respectively.
+ coil_trans double(4,4) Initially, transformation from the channel coordinates to device coordinates. This transformation is updated by calls to fiff_transform_meg_chs and fiff_transform_eeg_chs .
+ eeg_loc double(6) The location of the EEG electrode in coord_frame coordinates. The first three values contain the location of the electrode\]. If six values are present, the remaining ones indicate the location of the reference electrode for this channel.
+ coord_frame int32 Initially, the coordinate frame is FIFFV_COORD_DEVICE for MEG channels and FIFFV_COORD_HEAD for EEG channels.
+ unit int32 Unit of measurement. Relevant values are: 201 = T/m, 112 = T, 107 = V, and 202 = Am.
+ unit_mul int32 The data are given in unit s multiplied by 10unit_mul . Presently, unit_mul is always zero.
+ ch_name char\ Name of the channel.
+ coil_def coildef The coil definition structure. This is present only if mne_add_coil_defs has been successfully called.
+ ============== ============== =======================================================================================================================================================================================================================================================================================================================================================
+
+.. _BGBCJHJB:
+
+.. table:: The proj structure.
+
+ ========= =============== =========================================================================================================================================================
+ Field Data type Description
+ ========= =============== =========================================================================================================================================================
+ kind int32 The type of the projection item. Possible values are listed in :ref:`BGBJHCGD`. Look for entries starting with FIFFV_PROJ_ITEM or FIFFV_MNE_PROJ_ITEM.
+ active int32 Is this item active, i.e. , applied or about to be applied to the data.
+ data named matrix The projection vectors. The column names indicate the names of the channels associated to the elements of the vectors.
+ ========= =============== =========================================================================================================================================================
+
+.. _BGBJDIFD:
+
+.. table:: The comp structure.
+
+ ================== =============== ===========================================================================================================================================================================================================
+ Field Data type Description
+ ================== =============== ===========================================================================================================================================================================================================
+ ctfkind int32 The kind of the compensation as stored in file.
+ kind int32 ctfkind mapped into small integer numbers.
+ save_calibrated logical Were the compensation data saved in calibrated form. If this field is false, the matrix will be decalibrated using the fields row_cals and col_cals when the compensation data are saved by the toolbox.
+ row_cals double\ Calibration factors applied to the rows of the compensation data matrix when the data were read.
+ col_cals double\ Calibration factors applied to the columns of the compensation data matrix when the data were read.
+ data named matrix The compensation data matrix. The row_names list the names of the channels to which this compensation applies and the col_names the compensation channels. For more information, see Section 9.2.4
+ ================== =============== ===========================================================================================================================================================================================================
+
+.. _BGBFHDIJ:
+
+.. table:: The meas info structure.
+
+ ============= ============== =====================================================================================================================
+ Field Data type Description
+ ============= ============== =====================================================================================================================
+ file_id id The fif ID of the measurement file.
+ meas_id id The ID assigned to this measurement by the acquisition system or during file conversion.
+ nchan int32 Number of channels
+ sfreq double Sampling frequency
+ highpass double Highpass corner frequency\z]. Zero indicates a DC recording.
+ lowpass double Lowpass corner frequency\z].
+ chs ch (nchan) An array of channel information structures.
+ ch_names cell(nchan) Cell array of channel names.
+ dev_head_t trans The device to head transformation
+ ctf_head_t trans The transformation from 4D/CTF head coordinates to Neuromag head coordinates. This is only present in 4D/CTF data.
+ dev_ctf_t trans The transformation from device coordinates to 4D/CTF head coordinates. This is only present in 4D/CTF data
+ dig dig \ The Polhemus digitization data in head coordinates.
+ bads cell\ Bad channel list
+ projs proj \ SSP operator data.
+ comps comp \ Software gradient compensation data.
+ ============= ============== =====================================================================================================================
+
+.. _BGBEFJCB:
+
+.. table:: The surf structure.
+
+ =============== ================== ============================================================================================================================================================================================================================================================================
+ Field Data type Description
+ =============== ================== ============================================================================================================================================================================================================================================================================
+ id int32 The surface ID
+ sigma double The electrical conductivity of the compartment bounded by this surface. This field is present in BEM surfaces only.
+ np int32 Number of vertices on the surface
+ ntri int32 Number of triangles on the surface
+ coord_frame int32 Coordinate frame in which the locations and orientations are expressed.
+ rr double(np,3) The vertex locations
+ nn double(np,3) The vertex normals. If derived surface data was not requested, this is empty.
+ tris int32(ntri,3) Vertex numbers of the triangles in counterclockwise order as seen from the outside.
+ nuse int32 Number of active vertices, *i.e.*, vertices included in a decimated source space.
+ inuse int32(np) Which vertices are in use.
+ vertno int32(nuse) Indices of the vertices in use.
+ curv double(np) Curvature values at the vertices. If curvature information was not requested, this field is empty or absent.
+ tri_area double(ntri) The triangle areas in m2.If derived surface data was not requested, this field will be missing.
+ tri_cent double(ntri,3) The triangle centroids. If derived surface data was not requested, this field will be missing.
+ tri_nn double(ntri,3) The triangle normals. If derived surface data was not requested, this field will be missing.
+ nuse_tri int32 Number of triangles in use. This is present only if the surface corresponds to a source space created with the ``--ico`` option.
+ use_tris int32(nuse_tri) The vertices of the triangles in use in the complete triangulation. This is present only if the surface corresponds to a source space created with the ``--ico`` option.
+ nearest int32(np) This field is present only if patch information has been computed for a source space. For each vertex in the triangulation, these values indicate the nearest active source space vertex.
+ nearest_dist double(np) This field is present only if patch information has been computed for a source space. For each vertex in the triangulation, these values indicate the distance to the nearest active source space vertex.
+ dist double(np,np) Distances between vertices on this surface given as a sparse matrix. A zero off-diagonal entry in this matrix indicates that the corresponding distance has not been calculated.
+ dist_limit double The value given to mne_add_patch_info with the --dist option, see Section 11.7.2. This value is presently always negative, indicating that only distances between active source space vertices, as indicated by the vertno field of this structure, have been calculated.
+ =============== ================== ============================================================================================================================================================================================================================================================================
+
+.. _BGBJJIED:
+
+.. table:: The cov structure.
+
+ ========= ================== ======================================================================================================
+ Field Data type Description
+ ========= ================== ======================================================================================================
+ kind double What kind of a covariance matrix (1 = noise covariance, 2 = source covariance).
+ diag double Is this a diagonal matrix.
+ dim int32 Dimension of the covariance matrix.
+ names cell\ Names of the channels associated with the entries (may be empty).
+ data double(dim,dim) The covariance matrix. This a double(dim) vector for a diagonal covariance matrix.
+ projs proj \ The SSP vectors applied to these data.
+ bads cell\ Bad channel names.
+ nfree int32 Number of data points used to compute this matrix.
+ eig double(dim) The eigenvalues of the covariance matrix. This field may be empty for a diagonal covariance matrix.
+ eigvec double(dim,dim) The eigenvectors of the covariance matrix.
+ ========= ================== ======================================================================================================
+
+.. _BGBFJIBJ:
+
+.. table:: The fwd structure.
+
+ ============== ==================== =============================================================================================================================================================================================================================
+ Field Data type Description
+ ============== ==================== =============================================================================================================================================================================================================================
+ source_ori int32 Has the solution been computed for the current component normal to the cortex only (1) or all three source orientations (2).
+ coord_frame int32 Coordinate frame in which the locations and orientations are expressed.
+ nsource int32 Total number of source space points.
+ nchan int32 Number of channels.
+ sol named matrix The forward solution matrix.
+ sol_grad named matrix The derivatives of the forward solution with respect to the dipole location coordinates, see Section 5.9.6. This field is present only if the forward solution was computed with the ``--grad`` option, see Section 5.9.2.
+ mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame.
+ src surf \ The description of the source spaces
+ source_rr double(nsource,3) The source locations.
+ source_nn double\3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations).
+ ============== ==================== =============================================================================================================================================================================================================================
+
+.. _BGBIEIJE:
+
+.. table:: The inv structure. Note: The fields proj , whitener , reginv , and noisenorm are filled in by the routine mne_prepare_inverse_operator.
+
+ =============== ====================== ==============================================================================================================================================================
+ Field Data type Description
+ =============== ====================== ==============================================================================================================================================================
+ methods int32 Has the solution been computed using MEG data (1), EEG data (2), or both (3).
+ source_ori int32 Has the solution been computed for the current component normal to the cortex only (1) or all three source orientations (2)
+ nsource int32 Total number of source space points.
+ nchan int32 Number of channels.
+ coord_frame int32 Coordinate frame in which the locations and orientations are expressed.
+ source_nn double\3) The source orientations. Number of rows is either nsource (fixed source orientations) or 3*nsource (all source orientations).
+ sing double(nchan) The singular values, *i.e.*, the diagonal values of INLINE_EQUATION, see Section 6.2.5.
+ eigen_leads double\nchan) The matrix INLINE_EQUATION, see Section 6.2.5.
+ eigen_fields double(nchan,nchan) The matrix INLINE_EQUATION, see Section 6.2.5.
+ noise_cov cov The noise covariance matrix C.
+ source_cov cov The source covariance matrix R.
+ src surf \ The description of the source spaces
+ mri_head_t trans Transformation from the MRI coordinate frame to the (Neuromag) head coordinate frame.
+ nave double The number of averages.
+ projs proj \ The SSP vectors which were active when the decomposition was computed
+ proj double(nchan) The projection operator computed using projs .
+ whitener A sparse matrix containing the noise normalization factors. Dimension is either nsource (fixed source orientations) or 3*nsource (all source orientations).
+ reginv double(nchan) The diagonal matrix INLINE_EQUATION, see Section 6.2.5.
+ noisenorm double\*) A sparse matrix containing the noise normalization factors. Dimension is either nsource (fixed source orientations) or 3*nsource (all source orientations).
+ =============== ====================== ==============================================================================================================================================================
+
+On-line documentation for individual routines
+#############################################
+
+Each of the routines listed in Tables :ref:`BGBCGHAG` - :ref:`BGBEFADJ` has on-line documentation accessible by saying ``help`` <routine name> in Matlab.
diff --git a/doc/source/manual/mne.rst b/doc/source/manual/mne.rst
new file mode 100644
index 0000000..11b89a1
--- /dev/null
+++ b/doc/source/manual/mne.rst
@@ -0,0 +1,1323 @@
+
+
+.. _CBBDEAAI:
+
+=====================
+The current estimates
+=====================
+
+Overview
+########
+
+This Chapter describes the computation of the minimum-norm
+estimates. This is accomplished with two programs: *mne_inverse_operator* and *mne_make_movie*.
+The chapter starts with a mathematical description of the method,
+followed by description of the two software modules. The interactive
+program for inspecting data and inverse solutions, mne_analyze ,
+is covered in Chapter 7.
+
+.. _CBBDJFBJ:
+
+Minimum-norm estimates
+######################
+
+This section describes the mathematical details of the calculation
+of minimum-norm estimates. In Bayesian sense, the ensuing current
+distribution is the maximum a posteriori (MAP) estimate under the
+following assumptions:
+
+- The viable locations of the currents
+ are constrained to the cortex. Optionally, the current orientations
+ can be fixed to be normal to the cortical mantle.
+
+- The amplitudes of the currents have a Gaussian prior distribution
+ with a known source covariance matrix.
+
+- The measured data contain additive noise with a Gaussian distribution with
+ a known covariance matrix. The noise is not correlated over time.
+
+The linear inverse operator
+===========================
+
+The measured data in the source estimation procedure consists
+of MEG and EEG data, recorded on a total of N channels. The task
+is to estimate a total of M strengths of sources located on the
+cortical mantle. If the number of source locations is P, M = P for
+fixed-orientation sources and M = 3P if the source orientations
+are unconstrained. The regularized linear inverse operator following
+from the Bayesian approach is given by the INLINE_EQUATION matrix
+
+.. math:: 1 + 1 = 2
+
+where G is the gain matrix relating the source strengths
+to the measured MEG/EEG data, C is the data noise-covariance matrix
+and INLINE_EQUATION is the source covariance matrix.
+The dimensions of these matrices are INLINE_EQUATION, INLINE_EQUATION,
+and INLINE_EQUATION, respectively. The INLINE_EQUATION source-strength
+vector is obtained by multiplying the INLINE_EQUATION data
+vector by M.
+
+The expected value of the current amplitudes at time *t* is
+then given by INLINE_EQUATION, where INLINE_EQUATION is
+a vector containing the measured MEG and EEG data values at time *t*.
+
+.. _CBBHAAJJ:
+
+Regularization
+==============
+
+The a priori variance of the currents is, in practise, unknown.
+We can express this by writing INLINE_EQUATION,
+which yields the inverse operator
+
+.. math:: 1 + 1 = 2
+
+where the unknown current amplitude is now interpreted in
+terms of the regularization parameter INLINE_EQUATION.
+Small INLINE_EQUATION corresponds to large current amplitudes
+and complex estimate current patterns while a large INLINE_EQUATION means the
+amplitude of the current is limited and a simpler, smooth, current
+estimate is obtained.
+
+We can arrive in the regularized linear inverse operator
+also by minimizing the cost function
+
+.. math:: 1 + 1 = 2
+
+where the first term consists of the difference between the
+whitened measured data (see :ref:`CHDDHAGE`) and those predicted
+by the model while the second term is a weighted-norm of the current
+estimate. It is seen that, with increasing INLINE_EQUATION,
+the source term receive more weight and larger discrepancy between
+the measured and predicted data is tolerable.
+
+.. _CHDDHAGE:
+
+Whitening and scaling
+=====================
+
+The MNE software employs data whitening so that a 'whitened' inverse operator
+assumes the form
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION is the spatially
+whitened gain matrix. The expected current values are INLINE_EQUATION,
+where INLINE_EQUATION is a the whitened measurement
+vector at *t*. The spatial whitening operator
+is obtained with the help of the eigenvalue decomposition INLINE_EQUATION as INLINE_EQUATION.
+In the MNE software the noise-covariance matrix is stored as the
+one applying to raw data. To reflect the decrease of noise due to
+averaging, this matrix, INLINE_EQUATION, is scaled
+by the number of averages, *L*, *i.e.*, INLINE_EQUATION.
+
+As shown above, regularization of the inverse solution is
+equivalent to a change in the variance of the current amplitudes
+in the Bayesian *a priori* distribution.
+
+Convenient choice for the source-covariance matrix INLINE_EQUATION is
+such that INLINE_EQUATION. With this choice we
+can approximate INLINE_EQUATION, where SNR is
+the (power) signal-to-noise ratio of the whitened data.
+
+.. note:: The definition of the signal to noise-ratio/INLINE_EQUATION relationship given above works nicely for the whitened forward solution. In the un-whitened case scaling with the trace ratio INLINE_EQUATION does not make sense, since the diagonal elements summed have, in general, different units of measure. For example, the MEG data are expressed in T or T/m whereas the unit of EEG is Volts.
+
+.. _CBBHEGAB:
+
+Regularization of the noise-covariance matrix
+=============================================
+
+Since finite amount of data is usually available to compute
+an estimate of the noise-covariance matrix INLINE_EQUATION,
+the smallest eigenvalues of its estimate are usually inaccurate
+and smaller than the true eigenvalues. Depending on the seriousness
+of this problem, the following quantities can be affected:
+
+- The model data predicted by the current
+ estimate,
+
+- Estimates of signal-to-noise ratios, which lead to estimates
+ of the required regularization, see :ref:`CBBHAAJJ`,
+
+- The estimated current values, and
+
+- The noise-normalized estimates, see :ref:`CBBEAICH`.
+
+Fortunately, the latter two are least likely to be affected
+due to regularization of the estimates. However, in some cases especially
+the EEG part of the noise-covariance matrix estimate can be deficient, *i.e.*,
+it may possess very small eigenvalues and thus regularization of
+the noise-covariance matrix is advisable.
+
+The MNE software accomplishes the regularization by replacing
+a noise-covariance matrix estimate INLINE_EQUATION with
+
+.. math:: 1 + 1 = 2
+
+where the index INLINE_EQUATION goes across
+the different channel groups (MEG planar gradiometers, MEG axial
+gradiometers and magnetometers, and EEG), INLINE_EQUATION are
+the corresponding regularization factors, INLINE_EQUATION are
+the average variances across the channel groups, and INLINE_EQUATION are
+diagonal matrices containing ones at the positions corresponding
+to the channels contained in each channel group. The values INLINE_EQUATION can
+be adjusted with the regularization options ``--magreg`` , ``--gradreg`` ,
+and ``--eegreg`` specified at the time of the inverse operator
+decomposition, see :ref:`CBBDDBGF`. The convenience script mne_do_inverse_solution has
+the ``--magreg`` and ``--gradreg`` combined to
+a sigle option, ``--megreg`` , see Section 3.13.
+Suggested range of values for INLINE_EQUATION is INLINE_EQUATION.
+
+.. _CHDBEHBC:
+
+Computation of the solution
+===========================
+
+The most straightforward approach to calculate the MNE is
+to employ expression for the original or whitened inverse operator
+directly. However, for computational convenience we prefer to take
+another route, which employs the singular-value decomposition (SVD)
+of the matrix
+
+.. math:: 1 + 1 = 2
+
+where the superscript **INLINE_EQUATION indicates a
+square root of INLINE_EQUATION. For a diagonal matrix,
+one simply takes the square root of INLINE_EQUATION while
+in the more general case one can use the Cholesky factorization INLINE_EQUATION and
+thus INLINE_EQUATION.
+
+With the above SVD it is easy to show that
+
+.. math:: 1 + 1 = 2
+
+where the elements of the diagonal matrix INLINE_EQUATION are
+
+.. math:: 1 + 1 = 2
+
+With INLINE_EQUATION the expression for
+the expected current is
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION, INLINE_EQUATION being
+the kth column of V. It is thus seen that the current estimate is
+a weighted sum of the 'modified' eigenleads INLINE_EQUATION.
+
+It is easy to see that INLINE_EQUATION.
+To maintain the relation INLINE_EQUATION when INLINE_EQUATION changes
+we must have INLINE_EQUATION. With this approach, INLINE_EQUATION is
+independent of INLINE_EQUATION and, for fixed INLINE_EQUATION,
+we see directly that INLINE_EQUATION is independent
+of INLINE_EQUATION.
+
+.. _CBBEAICH:
+
+Noise normalization
+===================
+
+The noise-normalized linear estimates introduced by Dale
+et al. require division of the expected current amplitude by its
+variance. Noise normalization serves three purposes:
+
+- It converts the expected current value
+ into a dimensionless statistical test variable. Thus the resulting
+ time and location dependent values are often referred to as dynamic
+ statistical parameter maps (dSPM).
+
+- It reduces the location bias of the estimates. In particular,
+ the tendency of the MNE to prefer superficial currents is eliminated.
+
+- The width of the point-spread function becomes less dependent
+ on the source location on the cortical mantle. The point-spread
+ is defined as the MNE resulting from the signals coming from a point
+ current source (a current dipole) located at a certain point on
+ the cortex.
+
+In practice, noise normalization requires the computation
+of the diagonal elements of the matrix
+
+.. math:: 1 + 1 = 2
+
+With help of the singular-value decomposition approach we
+see directly that
+
+.. math:: 1 + 1 = 2
+
+Under the conditions expressed at the end of :ref:`CHDBEHBC`, it follows that the t-statistic values associated
+with fixed-orientation sources) are thus proportional to INLINE_EQUATION while
+the F-statistic employed with free-orientation sources is proportional
+to INLINE_EQUATION, correspondingly.
+
+.. note:: A section discussing statistical considerations related to the noise normalization procedure will be added to this manual in one of the subsequent releases.
+
+.. note:: The MNE software usually computes the square roots of the F-statistic to be displayed on the inflated cortical surfaces. These are also proportional to INLINE_EQUATION.
+
+.. _CHDCACDC:
+
+Predicted data
+==============
+
+Under noiseless conditions the SNR is infinite and thus leads
+to INLINE_EQUATION and the minimum-norm estimate
+explains the measured data perfectly. Under realistic conditions,
+however, INLINE_EQUATION and there is a misfit
+between measured data and those predicted by the MNE. Comparison
+of the predicted data, here denoted by INLINE_EQUATION,
+and measured one can give valuable insight on the correctness of
+the regularization applied.
+
+In the SVD approach we easily find
+
+.. math:: 1 + 1 = 2
+
+where the diagonal matrix INLINE_EQUATION has
+elements INLINE_EQUATION The predicted data is
+thus expressed as the weighted sum of the 'recolored eigenfields' in INLINE_EQUATION.
+
+.. _CBBDBHDI:
+
+Cortical patch statistics
+=========================
+
+If the ``--cps`` option was used in source space
+creation (see Section 3.5) or if mne_add_patch_info described
+in Section 11.7 was run manually the source space file
+will contain for each vertex of the cortical surface the information
+about the source space point closest to it as well as the distance
+from the vertex to this source space point. The vertices for which
+a given source space point is the nearest one define the cortical
+patch associated with with the source space point. Once these data
+are available, it is straightforward to compute the following cortical
+patch statistics (CPS) for each source location INLINE_EQUATION:
+
+- The average over the normals of at the
+ vertices in a patch, INLINE_EQUATION,
+
+- The areas of the patches, INLINE_EQUATION,
+ and
+
+- The average deviation of the vertex normals in a patch from
+ their average, INLINE_EQUATION, given in degrees.
+
+The orientation constraints
+===========================
+
+The principal sources of MEG and EEG signals are generally
+believed to be postsynaptic currents in the cortical pyramidal neurons.
+Since the net primary current associated with these microscopic
+events is oriented normal to the cortical mantle, it is reasonable
+to use the cortical normal orientation as a constraint in source
+estimation. In addition to allowing completely free source orientations,
+the MNE software implements three orientation constraints based
+of the surface normal data:
+
+- Source orientation can be rigidly fixed
+ to the surface normal direction (the ``--fixed`` option).
+ If cortical patch statistics are available the average normal over
+ each patch, INLINE_EQUATION, are used to define
+ the source orientation. Otherwise, the vertex normal at the source
+ space location is employed.
+
+- A *location independent or fixed loose orientation
+ constraint* (fLOC) can be employed (the ``--loose`` option).
+ In this approach, a source coordinate system based on the local
+ surface orientation at the source location is employed. By default,
+ the three columns of the gain matrix G, associated with a given
+ source location, are the fields of unit dipoles pointing to the
+ directions of the x, y, and z axis of the coordinate system employed
+ in the forward calculation (usually the MEG head coordinate frame).
+ For LOC the orientation is changed so that the first two source
+ components lie in the plane normal to the surface normal at the source
+ location and the third component is aligned with it. Thereafter, the
+ variance of the source components tangential to the cortical surface are
+ reduced by a factor defined by the ``--loose`` option.
+
+- A *variable loose orientation constraint* (vLOC)
+ can be employed (the ``--loosevar`` option). This is similar
+ to fLOC except that the value given with the ``--loosevar`` option
+ will be multiplied by INLINE_EQUATION, defined above.
+
+.. _CBBDFJIE:
+
+Depth weighting
+===============
+
+The minimum-norm estimates have a bias towards superficial
+currents. This tendency can be alleviated by adjusting the source
+covariance matrix R to favor deeper source locations. In the depth
+weighting scheme employed in MNE analyze, the elements of R corresponding
+to the INLINE_EQUATION source location are be
+scaled by a factor
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION are the three colums
+of INLINE_EQUATION corresponding to source location INLINE_EQUATION and INLINE_EQUATION is
+the order of the depth weighting, specified with the ``--weightexp`` option
+to mne_inverse_operator . The
+maximal amount of depth weighting can be adjusted ``--weightlimit`` option.
+
+.. _CBBDIJHI:
+
+fMRI-guided estimates
+=====================
+
+The fMRI weighting in MNE software means that the source-covariance matrix
+is modified to favor areas of significant fMRI activation. For this purpose,
+the fMRI activation map is thresholded first at the value defined by
+the ``--fmrithresh`` option to mne_do_inverse_operator or mne_inverse_operator .
+Thereafter, the source-covariance matrix values corresponding to
+the the sites under the threshold are multiplied by INLINE_EQUATION, set
+by the ``--fmrioff`` option.
+
+It turns out that the fMRI weighting has a strong influence
+on the MNE but the noise-normalized estimates are much less affected
+by it.
+
+.. _CBBDGIAE:
+
+Effective number of averages
+############################
+
+It is often the case that the epoch to be analyzed is a linear
+combination over conditions rather than one of the original averages
+computed. As stated above, the noise-covariance matrix computed
+is originally one corresponding to raw data. Therefore, it has to
+be scaled correctly to correspond to the actual or effective number
+of epochs in the condition to be analyzed. In general, we have
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION is the effective
+number of averages. To calculate INLINE_EQUATION for
+an arbitrary linear combination of conditions
+
+.. math:: 1 + 1 = 2
+
+we make use of the the fact that the noise-covariance matrix
+
+.. math:: 1 + 1 = 2
+
+which leads to
+
+.. math:: 1 + 1 = 2
+
+An important special case of the above is a weighted average,
+where
+
+.. math:: 1 + 1 = 2
+
+and, therefore
+
+.. math:: 1 + 1 = 2
+
+Instead of a weighted average, one often computes a weighted
+sum, a simplest case being a difference or sum of two categories.
+For a difference INLINE_EQUATION and INLINE_EQUATION and
+thus
+
+.. math:: 1 + 1 = 2
+
+or
+
+.. math:: 1 + 1 = 2
+
+Interestingly, the same holds for a sum, where INLINE_EQUATION.
+Generalizing, for any combination of sums and differences, where INLINE_EQUATION or INLINE_EQUATION , INLINE_EQUATION,
+we have
+
+.. math:: 1 + 1 = 2
+
+.. _CBBDDBGF:
+
+Inverse-operator decomposition
+##############################
+
+The program ``mne_inverse_operator`` calculates
+the decomposition INLINE_EQUATION, described in :ref:`CHDBEHBC`. It is normally invoked from the convenience
+script ``mne_do_inverse_operator`` . This section describes
+the options to ``mne_inverse_operator`` should a user need
+to invoke it directly for special-purpose processing.
+
+The command-line options of ``mne_inverse_operator`` are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---meg**
+
+ Employ MEG data in the calculation of the estimates.
+
+**\---eeg**
+
+ Employ EEG data in the calculation of the estimates. Note: The EEG
+ computations have not been throughly tested at this time.
+
+**\---fixed**
+
+ Use fixed source orientations normal to the cortical mantle. By default,
+ the source orientations are not constrained.
+
+**\---loose <amount>**
+
+ Employ a loose orientation constraint (LOC). This means that the source
+ covariance matrix entries corresponding to the current component
+ normal to the cortex are set equal to one and the transverse components
+ are set to <amount> . Recommended
+ value of amount is 0.2...0.6.
+
+**\---loosevar <amount>**
+
+ Use an adaptive loose orientation constraint. This option can be
+ only employed if the source spaces included in the forward solution
+ have the patch information computed, see Section 3.5. Blaa
+ blaa...
+
+**\---fwd <name>**
+
+ Specifies the name of the forward solution to use.
+
+**\---noisecov <name>**
+
+ Specifies the name of the noise-covariance matrix to use. If this
+ file contains a projection operator, attached by mne_browse_raw and mne_process_raw ,
+ no additional projection vectors can be added with the ``--proj`` option. For
+ backward compatibility, --senscov can be used as a synonym for --noisecov.
+
+**\---noiserank <value>**
+
+ Specifies the rank of the noise covariance matrix explicitly rather than
+ trying to reduce it automatically. This option is sheldom needed,
+
+**\---gradreg <value>**
+
+ Regularize the planar gradiometer section (channels for which the unit
+ of measurement is T/m) of the noise-covariance matrix by the given
+ amount. The value is restricted to the range 0...1. For details, see :ref:`CBBHEGAB`.
+
+**\---magreg <value>**
+
+ Regularize the magnetometer and axial gradiometer section (channels
+ for which the unit of measurement is T) of the noise-covariance matrix
+ by the given amount. The value is restricted to the range 0...1.
+ For details, see :ref:`CBBHEGAB`.
+
+**\---eegreg <value>**
+
+ Regularize the EEG section of the noise-covariance matrix by the given
+ amount. The value is restricted to the range 0...1. For details, see :ref:`CBBHEGAB`.
+
+**\---diagnoise**
+
+ Omit the off-diagonal terms from the noise-covariance matrix in
+ the computations. This may be useful if the amount of signal-free
+ data has been insufficient to calculate a reliable estimate of the
+ full noise-covariance matrix.
+
+**\---srccov <name>**
+
+ Specifies the name of the diagonal source-covariance matrix to use.
+ By default the source covariance matrix is a multiple of the identity matrix.
+ This option can be employed to incorporate the fMRI constraint.
+ The software to create a source-covariance matrix file from fMRI
+ data will be provided in a future release of this software package.
+
+**\---depth**
+
+ Employ depth weighting. For details, see Section :ref:`CBBDFJIE`.
+
+**\---weightexp <value>**
+
+ This parameter determines the steepness of the depth weighting function
+ (default = 0.8). For details, see Section :ref:`CBBDFJIE`.
+
+**\---weightlimit <value>**
+
+ Maximum relative strength of the depth weighting (default = 10). For
+ details, see Section :ref:`CBBDFJIE`.
+
+**\---fmri <name>**
+
+ With help of this w file, an *a priori* weighting
+ can be applied to the source covariance matrix. The source of the
+ weighting is usually fMRI but may be also some other data, provided
+ that the weighting can be expressed as a scalar value on the cortical
+ surface, stored in a w file. It is recommended that this w file
+ is appropriately smoothed (see Section 8.3) in mne_analyze , tksurfer or
+ with mne_smooth_w to contain
+ nonzero values at all vertices of the triangular tessellation of
+ the cortical surface. The name of the file given is used as a stem of
+ the w files. The actual files should be called <name> ``-lh.pri`` and <name> ``-rh.pri`` for
+ the left and right hemsphere weight files, respectively. The application
+ of the weighting is discussed in :ref:`CBBDIJHI`.
+
+**\---fmrithresh <value>**
+
+ This option is mandatory and has an effect only if a weighting function
+ has been specified with the ``--fmri`` option. If the value
+ is in the *a priori* files falls below this value
+ at a particular source space point, the source covariance matrix
+ values are multiplied by the value specified with the ``--fmrioff`` option
+ (default 0.1). Otherwise it is left unchanged.
+
+**\---fmrioff <value>**
+
+ The value by which the source covariance elements are multiplied
+ if the *a priori* weight falls below the threshold
+ set with ``--fmrithresh`` , see above.
+
+**\---bad <name>**
+
+ A text file to designate bad channels, listed one channel name on each
+ line of the file. If the noise-covariance matrix specified with the ``--noise`` cov option
+ contains projections, bad channel lists can be included only if
+ they specify all channels containing non-zero entries in a projection
+ vector. For example, bad channels can usually specify all magnetometers
+ or all gradiometers since the projection vectors for these channel
+ types are completely separate. Similarly, it is possible to include
+ MEG data only or EEG data only by using only one of ``--meg`` or ``--eeg`` options
+ since the projection vectors for MEG and EEG are always separate.
+
+**\---surfsrc**
+
+ Use a source coordinate system based on the local surface orientation
+ at the source location. By default, the three dipole components are
+ pointing to the directions of the x, y, and z axis of the coordinate system
+ employed in the forward calculation (usually the MEG head coordinate
+ frame). This option changes the orientation so that the first two
+ source components lie in the plane normal to the surface normal
+ at the source location and the third component is aligned with it.
+ If patch information is available in the source space, the normal
+ is the average patch normal, otherwise the vertex normal at the source
+ location is used. If the ``--loose`` or ``--loosevar`` option
+ is employed, ``--surfsrc`` is implied.
+
+**\---exclude <name>**
+
+ Exclude the source space points defined by the given FreeSurfer 'label' file
+ from the source reconstruction. This is accomplished by setting
+ the corresponding entries in the source-covariance matrix equal
+ to zero. The name of the file should end with ``-lh.label``
+ if it refers to the left hemisphere and with ``-rh.label`` if
+ it lists points in the right hemisphere, respectively.
+
+**\---proj <name>**
+
+ Include signal-space projection (SSP) information from this file. For information
+ on SSP, see Section 4.16. If the projections are present in
+ the noise-covariance matrix, the ``--proj`` option is
+ not allowed.
+
+**\---csd**
+
+ Compute the inverse operator for surface current densities instead
+ of the dipole source amplitudes. This requires the computation of patch
+ statistics for the source space. Since this computation is time consuming,
+ it is recommended that the patch statistics are precomputed and
+ the source space file containing the patch information is employed
+ already when the forward solution is computed, see Sections 3.5 and 3.11.
+ For technical details of the patch information, please consult :ref:`CBBDBHDI`. This option is considered experimental at
+ the moment.
+
+**\---inv <name>**
+
+ Save the inverse operator decomposition here.
+
+.. _CBBECEDE:
+
+Producing movies and snapshots
+##############################
+
+mne_make_movie is a program
+for producing movies and snapshot graphics frames without any graphics
+output to the screen. In addition, mne_make_movie can
+produce stc or w files which contain the numerical current estimate
+data in a simple binary format for postprocessing. These files can
+be displayed in mne_analyze ,
+see Chapter 7, utilized in the cross-subject averaging
+process, see Chapter 8, and read into Matlab using the MNE
+Matlab toolbox, see Chapter 10.
+
+The command-line options to mne_make_movie are
+explained in the following subsections.
+
+General options
+===============
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+Input files
+===========
+
+**\---inv <name>**
+
+ Load the inverse operator decomposition from here.
+
+**\---meas <name>**
+
+ Load the MEG or EEG data from this file.
+
+**\---set <number>**
+
+ The data set (condition) number to load. This is the sequential
+ number of the condition. You can easily see the association by looking
+ at the condition list in mne_analyze when
+ you load the file.
+
+**\---stcin <name>**
+
+ Specifies an stc file to read as input.
+
+Times and baseline
+==================
+
+**\---tmin <time/ms>**
+
+ Specifies the starting time employed in the analysis. If ``--tmin`` option
+ is missing the analysis starts from the beginning of the epoch.
+
+**\---tmax <time/ms>**
+
+ Specifies the finishing time employed in the analysis. If ``--tmax`` option
+ is missing the analysis extends to the end of the epoch.
+
+**\---tstep <step/ms>**
+
+ Time step between consequtive movie frames, specified in milliseconds.
+
+**\---integ < INLINE_EQUATION/ms>**
+
+ Integration time for each frame. Defaults to zero. The integration will
+ be performed on sensor data. If the time specified for a fram is INLINE_EQUATION,
+ the integration range will be INLINE_EQUATION.
+
+**\---pick <time/ms>**
+
+ Pick a time for the production of rgb, tif, jpg, png, or w files.
+ Several pick options may be present. The time must be with in the
+ analysis interval, indicated by the ``--tmin`` and ``--tmax`` options.
+ The ``--rgb`` , ``--tif`` , ``--jpg`` , ``--png`` , and ``--w`` options
+ control which file types are actually produced. When a ``--pick`` option
+ is encountered, the effect of any preceeding ``--pickrange`` option
+ is ignored.
+
+**\---pickrange**
+
+ All previous ``-pick`` options will be ignored. Instead,
+ snapshots are produced as indicated by the ``--tmin`` , ``--tmax`` ,
+ and ``--tstep`` options. This is useful, *e.g.*,
+ for producing input for scripts merging the individual graphics
+ snapshots into a composite "filmstrip" reprensentation.
+ However, such scripts are not yet part of the MNE software.
+
+**\---bmin <time/ms>**
+
+ Specifies the starting time of the baseline. In order to activate
+ baseline correction, both ``--bmin`` and ``--bmax`` options
+ must be present.
+
+**\---bmax <time/ms>**
+
+ Specifies the finishing time of the baseline.
+
+**\---baselines <file_name>**
+
+ Specifies a file which contains the baseline settings. Each line
+ of the file should contain a name of a channel, followed by the
+ baseline value, separated from the channel name by a colon. The
+ baseline values must be specified in basic units, i.e., Teslas/meter
+ for gradiometers, Teslas for magnetometers, and Volts for EEG channels.
+ If some channels are missing from the baseline file, warning messages are
+ issued: for these channels, the ``--bmin`` and ``--bmax`` settings will
+ be used.
+
+Options controlling the estimates
+=================================
+
+**\---nave <value>**
+
+ Specifies the effective number of averaged epochs in the input data, INLINE_EQUATION,
+ as discussed in :ref:`CBBDGIAE`. If the input data file is
+ one produced by mne_browse_raw or mne_process_raw , the
+ number of averages is correct in the file. However, if subtractions
+ or some more complicated combinations of simple averages are produced,
+ e.g., by using the xplotter software,
+ the number of averages should be manually adjusted along the guidelines
+ given in :ref:`CBBDGIAE`. This is accomplished either by
+ employing this flag or by adjusting the number of averages in the
+ data file with help of the utility mne_change_nave .
+
+**\---snr <value>**
+
+ An estimate for the amplitude SNR. The regularization parameter will
+ be set as INLINE_EQUATION. The default value is
+ SNR = 3. Automatic selection of the regularization parameter is
+ currently not supported.
+
+**\---spm**
+
+ Calculate the dSPM instead of the expected current value.
+
+**\---sLORETA**
+
+ Calculate the noise-normalized estimate using the sLORETA approach.
+ sLORETA solutions have in general a smaller location bias than either
+ the expected current (MNE) or the dSPM.
+
+**\---signed**
+
+ Indicate the current direction with respect to the cortex outer
+ normal by sign. Currents flowing out of the cortex are thus considered
+ positive (warm colors) and currents flowing into the cortex negative (cold
+ colors).
+
+**\---picknormalcomp**
+
+ The components of the estimates corresponding to directions tangential
+ with the cortical mantle are zeroed out.
+
+.. _CBBBBHIF:
+
+Visualization options
+=====================
+
+**\---subject <subject>**
+
+ Specifies the subject whose MRI data is employed in the visualization.
+ This must be the same subject that was used for computing the current
+ estimates. The environment variable SUBJECTS_DIR must be set to
+ point to a locations where the subjects are to be found.
+
+**\---morph <subject>**
+
+ Morph the data to to the cortical surface of another subject. The Quicktime
+ movie, stc-file, graphics snapshot, and w-file outputs are affected
+ by this option, *i.e.*, they will take the morphing
+ into account and will represent the data on the cortical surface
+ of the subject defined with this option. The stc files morphed to
+ a single subject's cortical surface are used by mne_average_estimates to
+ combine data from different subjects, see Section 8.6.
+ If morphing is selected appropriate smoothing must be specified
+ with the ``--smooth`` option. The morphing process can
+ be made faster by precomputing the necessary morphing maps with mne_make_morph_maps ,
+ see Section 8.4. More information about morphing and averaging
+ can be found in Chapter 8.
+
+**\---morphgrade <number>**
+
+ Adjusts the number of vertices in the stc files produced when morphing
+ is in effect. By default the number of vertices is 10242 corresponding
+ to --morphgrade value 5. Allowed values are 3, 4, 5, and 6 corresponding
+ to 642, 2562, 10242, and 40962 vertices, respectively.
+
+**\---surface <surface name>**
+
+ Name of the surface employed in the visualization. The default is inflated .
+
+**\---curv <name>**
+
+ Specify a nonstandard curvature file name. The default curvature files
+ are ``lh.curv`` and ``rh.curv`` . With this option,
+ the names become ``lh.`` <name> and ``rh.`` <name> .
+
+**\---patch <name> [:<angle/deg> ]**
+
+ Specify the name of a surface patch to be used for visualization instead
+ of the complete cortical surface. A complete name of a patch file
+ in the FreeSurface surf directory must be given. The name should
+ begin with lh or rh to allow association of the patch with a hemisphere.
+ Maximum of two --patch options can be in effect, one patch for each
+ hemisphere. If the name refers to a flat patch, the name can be
+ optionally followed by a colon and a rotation angle in degrees.
+ The flat patch will be then rotated counterclockwise by this amount
+ before display. You can check a suitable value for the rotation
+ angle by loading the patch interactively in mne_analyze .
+
+**\---width <value>**
+
+ Width of the graphics output frames in pixels. The default width
+ is 600 pixels.
+
+**\---height <value>**
+
+ Height of the graphics output frames in pixels. The default height
+ is 400 pixels.
+
+**\---mag <factor>**
+
+ Magnify the the visualized scene by this factor.
+
+**\---lh**
+
+ Select the left hemisphere for graphics output. By default, both hemisphere
+ are processed.
+
+**\---rh**
+
+ Select the right hemisphere for graphics output. By default, both hemisphere
+ are processed.
+
+**\---view <name>**
+
+ Select the name of the view for mov, rgb, and tif graphics output files.
+ The default viewnames, defined in ``$MNE_ROOT/share/mne/mne_analyze/eyes`` ,
+ are *lat* (lateral), *med* (medial), *ven* (ventral),
+ and *occ* (occipital). You can override these
+ defaults by creating the directory .mne under your home directory
+ and copying the eyes file there. Each line of the eyes file contais
+ the name of the view, the viewpoint for the left hemisphere, the
+ viewpoint for the right hemisphere, left hemisphere up vector, and
+ right hemisphere up vector. The entities are separated by semicolons.
+ Lines beginning with the pound sign (#) are considered to be comments.
+
+**\---smooth <nstep>**
+
+ Number of smoothsteps to take when producing the output frames. Depending
+ on the source space decimation, an appropriate number is 4 - 7.
+ Smoothing does not have any effect for the original brain if stc
+ files are produced. However, if morphing is selected smoothing is
+ mandatory even with stc output. For details of the smoothing procedure,
+ see Section 8.3.
+
+**\---nocomments**
+
+ Do not include the comments in the image output files or movies.
+
+**\---noscalebar**
+
+ Do not include the scalebar in the image output files or movies.
+
+**\---alpha <value>**
+
+ Adjust the opacity of maps shown on the cortical surface (0 = transparent,
+ 1 = totally opaque). The default value is 1.
+
+Thresholding
+============
+
+**\---fthresh <value>**
+
+ Specifies the threshold for the displayed colormaps. At the threshold,
+ the overlayed color will be equal to the background surface color.
+ For currents, the value will be multiplied byINLINE_EQUATION.
+ The default value is 8.
+
+**\---fmid <value>**
+
+ Specifies the midpoint for the displayed colormaps. At this value, the
+ overlayed color will be read (positive values) or blue (negative values).
+ For currents, the value will be multiplied byINLINE_EQUATION.
+ The default value is 15.
+
+**\---fmax <value>**
+
+ Specifies the maximum point for the displayed colormaps. At this value,
+ the overlayed color will bright yellow (positive values) or light
+ blue (negative values). For currents, the value will be multiplied
+ byINLINE_EQUATION. The default value is 20.
+
+**\---fslope <value>**
+
+ Included for backwards compatibility. If this option is specified
+ and ``--fmax`` option is *not* specified, INLINE_EQUATION.
+
+Output files
+============
+
+**\---mov <name>**
+
+ Produce QuickTime movie files. This is the 'stem' of
+ the ouput file name. The actual name is derived by stripping anything
+ upto and including the last period from the end of <name> .
+ According to the hemisphere, ``-lh`` or ``-rh`` is
+ then appended. The name of the view is indicated with ``-`` <viename> .
+ Finally, ``.mov`` is added to indicate a QuickTime output
+ file. The movie is produced for all times as dictated by the ``--tmin`` , ``--tmax`` , ``--tstep`` ,
+ and ``--integ`` options.
+
+**\---qual <value>**
+
+ Quality of the QuickTime movie output. The default quality is 80 and
+ allowed range is 25 - 100. The size of the movie files is a monotonously
+ increasing function of the movie quality.
+
+**\---rate <rate>**
+
+ Specifies the frame rate of the QuickTime movies. The default value is INLINE_EQUATION,
+ where INLINE_EQUATION is the time between subsequent
+ movie frames produced in seconds.
+
+**\---rgb <name>**
+
+ Produce rgb snapshots. This is the 'stem' of the
+ ouput file name. The actual name is derived by stripping anything
+ upto and including the last period from the end of <name> .
+ According to the hemisphere, ``-lh`` or ``-rh`` is
+ then appended. The name of the view is indicated with ``-`` <viename> .
+ Finally, ``.rgb`` is added to indicate an rgb output file.
+ Files are produced for all picked times as dictated by the ``--pick`` and ``--integ`` options.
+
+**\---tif <name>**
+
+ Produce tif snapshots. This is the 'stem' of the
+ ouput file name. The actual name is derived by stripping anything
+ upto and including the last period from the end of <name> .
+ According to the hemisphere, ``-lh`` or ``-rh`` is
+ then appended. The name of the view is indicated with ``-`` <viename> .
+ Finally, ``.tif`` is added to indicate an rgb output file.
+ Files are produced for all picked times as dictated by the ``--pick`` and ``--integ`` options.
+ The tif output files are *not* compressed. Pass
+ the files through an image processing program to compress them.
+
+**\---jpg <name>**
+
+ Produce jpg snapshots. This is the 'stem' of the
+ ouput file name. The actual name is derived by stripping anything
+ upto and including the last period from the end of <name> .
+ According to the hemisphere, ``-lh`` or ``-rh`` is
+ then appended. The name of the view is indicated with ``-`` <viename> .
+ Finally, ``.jpg`` is added to indicate an rgb output file.
+ Files are produced for all picked times as dictated by the ``--pick`` and ``--integ`` options.
+
+**\---png <name>**
+
+ Produce png snapshots. This is the 'stem' of the
+ ouput file name. The actual name is derived by stripping anything
+ upto and including the last period from the end of <name> .
+ According to the hemisphere, ``-lh`` or ``-rh`` is
+ then appended. The name of the view is indicated with ``-`` <viename> .
+ Finally, ``.png`` is added to indicate an rgb output file.
+ Files are produced for all picked times as dictated by the ``--pick`` and ``--integ`` options.
+
+**\---w <name>**
+
+ Produce w file snapshots. This is the 'stem' of
+ the ouput file name. The actual name is derived by stripping anything
+ upto and including the last period from the end of <name> .
+ According to the hemisphere, ``-lh`` .w or ``-rh`` .w
+ is then appended. Files are produced for all picked times as dictated
+ by the ``--pick`` and ``--integ`` options.
+
+**\---stc <name>**
+
+ Produce stc files for either the original subject or the one selected with
+ the ``--morph`` option. These files will contain data only
+ for the decimated locations. If morphing is selected, appropriate
+ smoothing is mandatory. The morphed maps will be decimated with
+ help of a subdivided icosahedron so that the morphed stc files will
+ always contain 10242 vertices. These morphed stc files can be easily
+ averaged together, e.g., in Matlab since they always contain an
+ identical set of vertices.
+
+**\---norm <name>**
+
+ Indicates that a separate w file
+ containing the noise-normalization values will be produced. The
+ option ``--spm`` must also be present. Nevertheless, the
+ movies and stc files output will
+ contain MNE values. The noise normalization data files will be called <name>-<SNR> ``-lh.w`` and <name>-<SNR> ``-rh.w`` .
+
+.. _CBBHHCEF:
+
+Label processing
+================
+
+**\---label <name>**
+
+ Specifies a label file to process. For each label file, the values
+ of the computed estimates are listed in text files. The label files
+ are produced by tksurfer or mne_analyze and
+ specify regions of interests (ROIs). A label file name should end
+ with ``-lh.label`` for left-hemisphere ROIs and with ``-rh.label`` for
+ right-hemisphere ones. The corresponding output files are tagged
+ with ``-lh-`` <data type> ``.amp`` and ``-rh-`` <data type> ``.amp`` , respectively. <data type> equals ``'mne`` ' for
+ expected current data and ``'spm`` ' for
+ dSPM data. Each line of the output file contains the waveform of
+ the output quantity at one of the source locations falling inside
+ the ROI. For more information about the label output formats, see Section 7.13.3.1.
+
+**\---labelcoords**
+
+ Include coordinates of the vertices in the output. The coordinates will
+ be listed in millimeters in the coordinate system which was specified
+ for the forward model computations. This option cannot be used with
+ stc input files (``--stcin`` ) because the stc files do
+ not contain the coordinates of the vertices.
+
+**\---labelverts**
+
+ Include vertex numbers in the output. The numbers refer to the complete
+ triangulation of the corresponding surface and are zero based. The
+ vertex numbers are by default on the first row or first column of the
+ output file depending on whether or not the ``--labeltimebytime`` option
+ is present.
+
+**\---labeltimebytime**
+
+ Output the label data time by time instead of the default vertex-by-vertex
+ output.
+
+**\---labeltag <tag>**
+
+ End the output files with the specified tag. By default, the output files
+ will end with ``-mne.amp`` or ``-spm.amp`` depending
+ on whether MNE or one of the noise-normalized estimates (dSPM or sLORETA)
+ was selected.
+
+**\---labeloutdir <directory>**
+
+ Specifies the directory where the output files will be located.
+ By default, they will be in the current working directory.
+
+**\---labelcomments**
+
+ Include comments in the output files. The comment lines begin with the
+ percent sign to make the files compatible with Matlab.
+
+**\---scaleby <factor>**
+
+ By default, the current values output to the files will be in the
+ actual physical units (Am). This option allows scaling of the current
+ values to other units. mne_analyze typically
+ uses 1e10 to bring the numbers to a human-friendly scale.
+
+Using stc file input
+====================
+
+The ``--stcin`` option allows input of stc files.
+This feature has several uses:
+
+- QuickTime movies can be produced from
+ existing stc files without having to resort to EasyMeg.
+
+- Graphics snapshot can be produced from existing stc files.
+
+- Existing stc files can be temporally resampled with help of
+ the ``--tmin`` , ``--tmax`` , ``--tstep`` ,
+ and ``--integ`` options.
+
+- Existing stc files can be morphed to another cortical surface
+ by specifying the ``--morph`` option.
+
+- Timecourses can be inquired and stored into text files with
+ help of the ``--label`` options, see above.
+
+.. _CBBCGHAH:
+
+Computing inverse from raw and evoked data
+##########################################
+
+The purpose of the utility mne_compute_raw_inverse is
+to compute inverse solutions from either evoked-response or raw
+data at specified ROIs (labels) and to save the results in a fif
+file which can be viewed with mne_browse_raw ,
+read to Matlab directly using the MNE Matlab Toolbox, see Chapter 10,
+or converted to Matlab format using either mne_convert_mne_data , mne_raw2mat ,
+or mne_epochs2mat , see Chapter 9.
+
+.. _CHDEIHFA:
+
+Command-line options
+====================
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---in <filename>**
+
+ Specifies the input data file. This can be either an evoked data
+ file or a raw data file.
+
+**\---bmin <time/ms>**
+
+ Specifies the starting time of the baseline. In order to activate
+ baseline correction, both ``--bmin`` and ``--bmax`` options
+ must be present. This option applies to evoked data only.
+
+**\---bmax <time/ms>**
+
+ Specifies the finishing time of the baseline. This option applies
+ to evoked data only.
+
+**\---set <number>**
+
+ The data set (condition) number to load. This is the sequential
+ number of the condition. You can easily see the association by looking
+ at the condition list in mne_analyze when
+ you load the file.
+
+**\---inv <name>**
+
+ Load the inverse operator decomposition from here.
+
+**\---nave <value>**
+
+ Specifies the effective number of averaged epochs in the input data, INLINE_EQUATION,
+ as discussed in :ref:`CBBDGIAE`. If the input data file is
+ one produced by mne_browse_raw or mne_process_raw ,
+ the number of averages is correct in the file. However, if subtractions
+ or some more complicated combinations of simple averages are produced,
+ e.g., by using the xplotter software,
+ the number of averages should be manually adjusted along the guidelines
+ given in :ref:`CBBDGIAE`. This is accomplished either by
+ employing this flag or by adjusting the number of averages in the
+ data file with help of the utility mne_change_nave .
+
+**\---snr <value>**
+
+ An estimate for the amplitude SNR. The regularization parameter will
+ be set as INLINE_EQUATION. The default value is
+ SNR = 3. Automatic selection of the regularization parameter is
+ currently not supported.
+
+**\---spm**
+
+ Calculate the dSPM instead of the expected current value.
+
+**\---picknormalcomp**
+
+ The components of the estimates corresponding to directions tangential
+ with the cortical mantle are zeroed out.
+
+**\---mricoord**
+
+ Provide source locations and orientations in the MRI coordinate frame
+ instead of the default head coordinate frame.
+
+**\---label <name>**
+
+ Specifies a label file to process. For each label file, the values
+ of the computed estimates stored in a fif file. For more details,
+ see :ref:`CBBHJDAI`. The label files are produced by tksurfer
+ or mne_analyze and specify regions
+ of interests (ROIs). A label file name should end with ``-lh.label`` for
+ left-hemisphere ROIs and with ``-rh.label`` for right-hemisphere
+ ones. The corresponding output files are tagged with ``-lh-`` <data type> ``.fif`` and ``-rh-`` <data type> ``.fif`` , respectively. <data type> equals ``'mne`` ' for expected
+ current data and ``'spm`` ' for dSPM data.
+ For raw data, ``_raw.fif`` is employed instead of ``.fif`` .
+ The output files are stored in the same directory as the label files.
+
+**\---labelselout**
+
+ Produces additional label files for each label processed, containing only
+ those vertices within the input label which correspond to available
+ source space vertices in the inverse operator. These files have the
+ same name as the original label except that ``-lh`` and ``-rh`` are replaced
+ by ``-sel-lh`` and ``-sel-rh`` , respectively.
+
+**\---align_z**
+
+ Instructs the program to try to align the waveform signs within
+ the label. For more information, see :ref:`CBBHJDAI`. This
+ flag will not have any effect if the inverse operator has been computed
+ with the strict orientation constraint active.
+
+**\---labeldir <directory>**
+
+ All previous ``--label`` options will be ignored when this
+ option is encountered. For each label in the directory, the output
+ file defined with the ``--out`` option will contain a summarizing
+ waveform which is the average of the waveforms in the vertices of
+ the label. The ``--labeldir`` option implies ``--align_z`` and ``--picknormalcomp`` options.
+
+**\---orignames**
+
+ This option is used with the ``--labeldir`` option, above.
+ With this option, the output file channel names will be the names
+ of the label files, truncated to 15 characters, instead of names
+ containing the vertex numbers.
+
+**\---out <name>**
+
+ Required with ``--labeldir`` . This is the output file for
+ the data.
+
+**\---extra <name>**
+
+ By default, the output includes the current estimate signals and
+ the digital trigger channel, see ``--digtrig`` option,
+ below. With the ``--extra`` option, a custom set of additional
+ channels can be included. The extra channel text file should contain
+ the names of these channels, one channel name on each line. With
+ this option present, the digital trigger channel is not included
+ unless specified in the extra channel file.
+
+**\---noextra**
+
+ No additional channels will be included with this option present.
+
+**\---digtrig <name>**
+
+ Name of the composite digital trigger channel. The default value
+ is 'STI 014'. Underscores in the channel name
+ will be replaced by spaces.
+
+**\---split <size/MB>**
+
+ Specifies the maximum size of the raw data files saved. By default, the
+ output is split into files which are just below 2 GB so that the
+ fif file maximum size is not exceed.
+
+.. note:: The digital trigger channel can also be set with the MNE_TRIGGER_CH_NAME environment variable. Underscores in the variable value will *not* be replaced with spaces by mne_compute_raw_inverse . Using the ``--digtrig`` option supersedes the MNE_TRIGGER_CH_NAME environment variable.
+
+.. _CBBHJDAI:
+
+Implementation details
+======================
+
+The fif files output from mne_compute_raw_inverse have
+various fields of the channel information set to facilitate interpretation
+by postprocessing software as follows:
+
+**channel name**
+
+ Will be set to J[xyz] <number> ,
+ where the source component is indicated by the coordinat axis name
+ and number is the vertex number, starting from zero, in the complete
+ triangulation of the hemisphere in question.
+
+**logical channel number**
+
+ Will be set to is the vertex number, starting from zero, in the
+ complete triangulation of the hemisphere in question.
+
+**sensor location**
+
+ The location of the vertex in head coordinates or in MRI coordinates,
+ determined by the ``--mricoord`` flag.
+
+**sensor orientation**
+
+ The *x*-direction unit vector will point to the
+ direction of the current. Other unit vectors are set to zero. Again,
+ the coordinate system in which the orientation is expressed depends
+ on the ``--mricoord`` flag.
+
+The ``--align_z`` flag tries to align the signs
+of the signals at different vertices of the label. For this purpose,
+the surface normals within the label are collected into a INLINE_EQUATION matrix.
+The preferred orientation will be taken as the first right singular
+vector of this matrix, corresponding to its largest singular value.
+If the dot product of the surface normal of a vertex is negative,
+the sign of the estimates at this vertex are inverted. The inversion
+is reflected in the current direction vector listed in the channel
+information, see above.
+
+.. note:: The raw data files output by mne_compute_raw_inverse can be converted to mat files with mne_raw2mat , see Section 9.13. Alternatively, the files can be read directly from Matlab using the routines in the MNE Matlab toolbox, see Chapter 10. The evoked data output can be easily read directly from Matlab using the fiff_load_evoked routine in the MNE Matlab toolbox. Both raw data and evoked output files can be loaded into mne_browse_raw , see Chapter 4.
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+++ b/doc/source/manual/morph.rst
@@ -0,0 +1,407 @@
+
+
+.. _CACCICGI:
+
+======================
+Morphing and averaging
+======================
+
+Overview
+########
+
+The spherical morphing of the surfaces accomplished by FreeSurfer can be
+employed to bring data from different subjects into a common anatomical
+frame. This chapter describes utilities which make use of the spherical morphing
+procedure. mne_morph_labels morphs
+label files between subjects allowing the definition of labels in
+a one brain and transforming them to anatomically analogous labels
+in another. mne_average_estimates offers
+the capability to compute averages of data computed with the MNE software
+across subjects.
+
+.. _CHDJDHII:
+
+The morphing maps
+#################
+
+The MNE software accomplishes morphing with help of morphing
+maps which can be either computed on demand or precomputed using mne_make_morph_maps ,
+see :ref:`CHDBBHDH`. The morphing is performed with help
+of the registered spherical surfaces (``lh.sphere.reg`` and ``rh.sphere.reg`` )
+which must be produced in FreeSurfer .
+A morphing map is a linear mapping from cortical surface values
+in subject A (INLINE_EQUATION) to those in another
+subject B (INLINE_EQUATION)
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION is a sparse matrix
+with at most three nonzero elements on each row. These elements
+are determined as follows. First, using the aligned spherical surfaces,
+for each vertex INLINE_EQUATION, find the triangle INLINE_EQUATIONon the
+spherical surface of subject A which contains the location INLINE_EQUATION.
+Next, find the numbers of the vertices of this triangle and set
+the corresponding elements on the *j*th row of INLINE_EQUATION so that INLINE_EQUATION will
+be a linear interpolation between the triangle vertex values reflecting
+the location INLINE_EQUATION within the triangle INLINE_EQUATION.
+
+It follows from the above definition that in general
+
+.. math:: 1 + 1 = 2
+
+*i.e.*,
+
+.. math:: 1 + 1 = 2
+
+even if
+
+.. math:: 1 + 1 = 2
+
+*i.e.*, the mapping is *almost* a
+bijection.
+
+.. _CHDEBAHH:
+
+About smoothing
+###############
+
+The current estimates are normally defined only in a decimated
+grid which is a sparse subset of the vertices in the triangular
+tessellation of the cortical surface. Therefore, any sparse set
+of values is distributed to neighboring vertices to make the visualized
+results easily understandable. This procedure has been traditionally
+called smoothing but a more appropriate name
+might be smudging or blurring in
+accordance with similar operations in image processing programs.
+
+In MNE software terms, smoothing of the vertex data is an
+iterative procedure, which produces a blurred image INLINE_EQUATIONfrom
+the original sparse image INLINE_EQUATION by applying
+in each iteration step a sparse blurring matrix:
+
+.. math:: 1 + 1 = 2
+
+On each row INLINE_EQUATIONof the matrix INLINE_EQUATIONthere
+are INLINE_EQUATION nonzero entries whose values
+equal INLINE_EQUATION. Here INLINE_EQUATION is
+the number of immediate neighbors of vertex INLINE_EQUATION which
+had non-zero values at iteration step INLINE_EQUATION.
+Matrix INLINE_EQUATION thus assigns the average
+of the non-zero neighbors as the new value for vertex INLINE_EQUATION.
+One important feature of this procedure is that it tends to preserve
+the amplitudes while blurring the surface image.
+
+Once the indices non-zero vertices in INLINE_EQUATION and
+the topology of the triangulation are fixed the matrices INLINE_EQUATION are
+fixed and independent of the data. Therefore, it would be in principle
+possible to construct a composite blurring matrix
+
+.. math:: 1 + 1 = 2
+
+However, it turns out to be computationally more effective
+to do blurring with an iteration. The above formula for INLINE_EQUATION also
+shows that the smudging (smoothing) operation is linear.
+
+.. _CHDBBHDH:
+
+Precomputing the morphing maps
+##############################
+
+The utility mne_make_morph_maps was
+created to assist mne_analyze and mne_make_movie in
+morphing. Since the morphing maps described above take a while to
+compute, it is beneficial to construct all necessary maps in advance
+before using mne_make_movie .
+The precomputed morphing maps are located in ``$SUBJECTS_DIR/morph-maps`` . mne_make_morph_maps creates
+this directory automatically if it does not exist. If this directory
+exists when mne_analyze or mne_make_movie is run
+and morphing is requested, the software first looks for already
+existing morphing maps there. Also, if mne_analyze or mne_make_movie have
+to recompute any morphing maps, they will be saved to ``$SUBJECTS_DIR/morph-maps`` if
+this directory exists.
+
+The names of the files in ``$SUBJECTS_DIR/morph-maps`` are
+of the form:
+
+<A> -<B> -``morph.fif`` ,
+
+where <A> and <B> are
+names of subjects. These files contain the maps for both hemispheres,
+and in both directions, *i.e.*, both INLINE_EQUATION and INLINE_EQUATION, as
+defined above. Thus the files <A> -<B> -``morph.fif`` or <B> -<A> -``morph.fif`` are
+functionally equivalent. The name of the file produced by mne_analyze or mne_make_movie depends
+on the role of <A> and <B> in
+the analysis.
+
+If you choose to compute the morphing maps in batch in advance,
+use mne_make_morph_maps , which
+accepts the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---redo**
+
+ Recompute the morphing maps even if they already exist.
+
+**\---from <subject>**
+
+ Compute morphing maps from this subject.
+
+**\---to <subject>**
+
+ Compute morphing maps to this subject.
+
+**\---all**
+
+ Do all combinations. If this is used without either ``--from`` or ``--to`` options,
+ morphing maps for all possible combinations are computed. If ``--from`` or ``--to`` is
+ present, only maps between the specified subject and all others
+ are computed.
+
+.. note:: Because all morphing map files contain maps in both directions, the choice of ``--from`` and ``--to`` options only affect the naming of the morphing map files to be produced. mne_make_morph_maps creates directory ``$SUBJECTS_DIR/morph-maps`` if necessary.
+
+.. _CHDCEAFC:
+
+Morphing label data
+###################
+
+In some instances it is desirable to use anatomically equivalent
+labels for all subjects in a study. This can be accomplished by
+creating a set of labels in one subject and morphing them to another
+subjects anatomy using the spherical morphing procedure. mne_morph_labels was
+created to facilitate this task. It has the following command-line
+options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---from <subject>**
+
+ Name of the subject for which the labels were originally defined.
+
+**\---to <subject>**
+
+ Name of the subject for which the morphed labels should be created.
+
+**\---labeldir <directory>**
+
+ A directory containing the labels to morph.
+
+**\---prefix <prefix>**
+
+ Adds <prefix> in the beginning
+ of the output label names. A dash will be inserted between <prefix> and
+ the rest of the name.
+
+**\---smooth <number>**
+
+ Apply smoothing with the indicated number of iteration steps (see :ref:`CHDEBAHH`) to the labels before morphing them. This is
+ advisable because otherwise the resulting labels may have little
+ holes in them since the morphing map is not a bijection. By default,
+ two smoothsteps are taken.
+
+As the labels are morphed, a directory with the name of the
+subject specified with the ``--to`` option is created under
+the directory specified with ``--labeldir`` to hold the
+morphed labels.
+
+.. _CHDFDIFE:
+
+Averaging
+#########
+
+Overview
+========
+
+As illustrated in :ref:`CHDDJBDH`, cross-subject averaging
+involves three straightforward steps:
+
+- Use mne_make_movie to
+ create stc files morphed to a single subject. This requires the
+ use of the ``--morph`` option, see Section 6.5.5.
+ The resulting files will have identical selections of vertices on
+ the cortical surface of the subject used in averaging. This step
+ can be speeded up by precomputing the morphing maps employed in
+ the process, see :ref:`CHDBBHDH`.
+
+- Employ mne_average_estimates or
+ a Matlab script to read the data from the stc files and to produce
+ an output stc file containing the averaged data. The MNE Matlab
+ toolbox routines for reading and writing stc files are documented
+ in Chapter 10.
+
+- Use mne_analyze or mne_make_movie to
+ visualize the result or use the stc files from the previous step
+ in your own Matlab routines in further processing.
+
+.. _CHDDJBDH:
+
+.. figure:: picture.png
+ :alt: none
+
+ Workflow of the cross-subject averaging process in MNE software. References in parenthesis indicate sections and chapters of this manual
+
+.. note:: The old utility mne_grand_average has been removed from the MNE software because of its inefficiency. All users should adopt the combination of mne_make_movie and mne_average_estimates instead.
+
+.. warning:: With the ``--ico`` option it is now possible to generate source spaces with equal number of vertices in each subject. This may lead to the wrong conclusion that stc data could be averaged without doing the morphing step first. Even with identical number vertices in the source spaces it is mandatory to process the data through mne_make_movie to create corresponding source locations before using mne_average_estimates .
+
+.. _CHDEHFGD:
+
+The averager
+============
+
+mne_average_estimates is
+the new utility for averaging data in stc files. It requires that
+all stc files represent data on one individual's cortical
+surface and contain identical sets of vertices. mne_average_estimates uses
+linear interpolation to resample data in time as necessary. The
+command line arguments are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---desc <filenname>**
+
+ Specifies the description file for averaging. The format of this
+ file is described below.
+
+The description file
+--------------------
+
+The description file for mne_average_estimates consists
+of a sequence of tokens, separated by whitespace (space, tab, or
+newline). If a token consists of several words it has to be enclosed
+in quotes. One or more tokens constitute an phrase, which has a
+meaning for the averaging definition. Any line starting with the
+pound sign (#) is a considered to be a comment line. There are two
+kinds of phrases in the description file: global and contextual.
+The global phrases have the same meaning independent on their location
+in the file while the contextual phrases have different effects depending
+on their location in the file.
+
+There are three types of contexts in the description file:
+the global context, an input context,
+and the output context. In the
+beginning of the file the context is global for
+defining global parameters. The input context
+defines one of the input files (subjects) while the output context
+specifies the destination for the average.
+
+The global phrases are:
+
+**tmin <value/ms>**
+
+ The minimum time to be considered. The output stc file starts at
+ this time point if the time ranges of the stc files include this
+ time. Otherwise the output starts from the next later available
+ time point.
+
+**tstep <step/ms>**
+
+ Time step between consecutive movie frames, specified in milliseconds.
+
+**tmax <value/ms>**
+
+ The maximum time point to be considered. A multiple of tstep will be
+ added to the first time point selected until this value or the last time
+ point in one of the input stc files is reached.
+
+**integ < INLINE_EQUATION/ms>**
+
+ Integration time for each frame. Defaults to zero. The integration will
+ be performed on sensor data. If the time specified for a frame is INLINE_EQUATION,
+ the integration range will be INLINE_EQUATION.
+
+**stc <filename>**
+
+ Specifies an input stc file. The filename can be specified with
+ one of the ``-lh.stc`` and ``-rh.stc`` endings
+ or without them. This phrase ends the present context and starts
+ an input context.
+
+**deststc <filename>**
+
+ Specifies the output stc file. The filename can be specified with
+ one of the ``-lh.stc`` and ``-rh.stc`` endings
+ or without them. This phrase ends the present context and starts
+ the output context.
+
+**lh**
+
+ Process the left hemisphere. By default, both hemispheres are processed.
+
+**rh**
+
+ Process the left hemisphere. By default, both hemispheres are processed.
+
+The contextual phrases are:
+
+**weight <value>**
+
+ Specifies the weight of the current data set. This phrase is valid
+ in the input and output contexts.
+
+**abs**
+
+ Specifies that the absolute value of the data should be taken. Valid
+ in all contexts. If specified in the global context, applies to
+ all subsequent input and output contexts. If specified in the input
+ or output contexts, applies only to the data associated with that
+ context.
+
+**pow <value>**
+
+ Specifies that the data should raised to the specified power. For
+ negative values, the absolute value of the data will be taken and
+ the negative sign will be transferred to the result, unless abs is
+ specified. Valid in all contexts. Rules of application are identical
+ to abs .
+
+**sqrt**
+
+ Means pow 0.5
+
+The effects of the options can be summarized as follows.
+Suppose that the description file includes INLINE_EQUATION contexts
+and the temporally resampled data are organized in matrices INLINE_EQUATION,
+where INLINE_EQUATION is the subject index, and
+the rows are the signals at different vertices of the cortical surface.
+The average computed by mne_average_estimates is
+then:
+
+.. math:: 1 + 1 = 2
+
+with
+
+.. math:: 1 + 1 = 2
+
+and
+
+.. math:: 1 + 1 = 2
+
+In the above, INLINE_EQUATION and INLINE_EQUATION are
+the powers and weights assigned to each of the subjects whereas INLINE_EQUATION and INLINE_EQUATION are
+the output weight and power value, respectively. The sign is either
+included (INLINE_EQUATION, INLINE_EQUATION)
+or omitted (INLINE_EQUATION, INLINE_EQUATION)
+depending on the presence of abs phrases in the description file.
+
+.. note:: mne_average_estimates requires that the number of vertices in the stc files are the same and that the vertex numbers are identical. This will be the case if the files have been produced in mne_make_movie using the ``--morph`` option.
+
+.. note:: It is straightforward to read and write stc files using the MNE Matlab toolbox described in Chapter 10 and thus write custom Matlab functions to realize more complicated custom group analysis tools.
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+
+
+.. _CACCICGI:
+
+==============
+Useful reading
+==============
+
+General MEG reviews
+###################
+
+M. Hämäläinen, R. Hari, R. Ilmoniemi,
+J. Knuutila, and O. V. Lounasmaa, "Magnetoencephalography - theory,
+instrumentation, and applications to noninvasive studies of the
+working human brain," Reviews of Modern Physics, vol. 65, pp. 413-497,
+1993.
+
+S. Baillet, J. C. Mosher, and R. M. Leahy, "Electromagnetic
+Brain Mapping," IEEE Signal Processing Magazine, vol. 18, pp. 14
+- 30, 2001.
+
+M. Hämäläinen and R. Hari, "Magnetoencephalographic
+Characterization of Dynamic Brain Activation: Basic Principles and
+Methods of Data Collection and Source Analysis," in Brain mapping
+: the methods, A. W. Toga and J. C. Mazziotta, Eds. Amsterdam ;
+Boston: Academic Press, 2002.
+
+Cortical surface reconstruction and morphing
+############################################
+
+A. M. Dale, B. Fischl, and M. I. Sereno, "Cortical surface-based
+analysis. I. Segmentation and surface reconstruction," Neuroimage,
+vol. 9, pp. 179-94., 1999.
+
+B. Fischl, M. I. Sereno, and A. M. Dale, "Cortical surface-based
+analysis. II: Inflation, flattening, and a surface-based coordinate
+system," Neuroimage, vol. 9, pp. 195-207., 1999.
+
+B. Fischl, M. I. Sereno, R. B. Tootell, and A. M. Dale, "High-resolution intersubject
+averaging and a coordinate system for the cortical surface," Hum
+Brain Mapp, vol. 8, pp. 272-84, 1999.
+
+.. _CEGEGDEI:
+
+Forward modeling
+################
+
+M. S. Hämäläinen and J. Sarvas,
+"Realistic conductivity geometry model of the human head for interpretation
+of neuromagnetic data," IEEE Trans. Biomed. Eng., vol. BME-36, pp.
+165-171, 1989.
+
+B. Fischl, D. H. Salat, A. J. van der Kouwe, N. Makris, F.
+Segonne, B. T. Quinn, and A. M. Dale, "Sequence-independent segmentation
+of magnetic resonance images," Neuroimage, vol. 23 Suppl 1, pp.
+S69-84, 2004.
+
+F. Segonne, A. M. Dale, E. Busa, M. Glessner, D. Salat, H.
+K. Hahn, and B. Fischl, "A hybrid approach to the skull stripping
+problem in MRI," Neuroimage, vol. 22, pp. 1060-75, Jul 2004.
+
+J. Jovicich, S. Czanner, D. Greve, E. Haley, A. van der Kouwe,
+R. Gollub, D. Kennedy, F. Schmitt, G. Brown, J. Macfall, B. Fischl,
+and A. Dale, "Reliability in multi-site structural MRI studies:
+effects of gradient non-linearity correction on phantom and human
+data," Neuroimage, vol. 30, pp. 436-43, 2006.
+
+J. C. Mosher, R. M. Leahy, and P. S. Lewis, "EEG and MEG:
+forward solutions for inverse methods," IEEE Trans Biomed Eng, vol.
+46, pp. 245-59, 1999.
+
+.. _CEGIEEBB:
+
+Signal-space projections
+########################
+
+C. D. Tesche, M. A. Uusitalo, R. J. Ilmoniemi, M. Huotilainen,
+M. Kajola, and O. Salonen, "Signal-space projections of MEG data
+characterize both distributed and well-localized neuronal sources,"
+Electroencephalogr Clin Neurophysiol, vol. 95, pp. 189-200, 1995.
+
+M. A. Uusitalo and R. J. Ilmoniemi, "Signal-space projection
+method for separating MEG or EEG into components," Med Biol Eng
+Comput, vol. 35, pp. 135-40, 1997.
+
+Minimum-norm estimates
+######################
+
+M. Hämäläinen and R. Ilmoniemi,
+"Interpreting magnetic fields of the brain: minimum norm estimates,"
+Helsinki University of Technology, Espoo TKK-F-A559, 1984.
+
+A. Dale and M. Sereno, "Improved localization of cortical
+activity by combining EEG and MEG with MRI cortical surface reconstruction:
+A linear approach," J. Cog. Neurosci, vol. 5, pp. 162-176, 1993.
+
+M. S. Hämäläinen and R. J. Ilmoniemi,
+"Interpreting magnetic fields of the brain: minimum norm estimates,"
+Med Biol Eng Comput, vol. 32, pp. 35-42., 1994.
+
+A. M. Dale, A. K. Liu, B. R. Fischl, R. L. Buckner, J. W.
+Belliveau, J. D. Lewine, and E. Halgren, "Dynamic statistical parametric
+mapping: combining fMRI and MEG for high-resolution imaging of cortical
+activity," Neuron, vol. 26, pp. 55-67, 2000.
+
+A. K. Liu, A. M. Dale, and J. W. Belliveau, "Monte Carlo
+simulation studies of EEG and MEG localization accuracy," Hum Brain
+Mapp, vol. 16, pp. 47-62, 2002.
+
+F. H. Lin, J. W. Belliveau, A. M. Dale, and M. S. Hamalainen,
+"Distributed current estimates using cortical orientation constraints,"
+Hum Brain Mapp, vol. 27, pp. 1-13, 2006.
+
+T. F. Oostendorp, J. Delbeke, and D. F. Stegeman, "The conductivity
+of the human skull: results of in vivo and in vitro measurements,"
+IEEE Trans Biomed Eng, vol. 47, pp. 1487-92, Nov 2000.
+
+S. I. Gonçalves, J. C. de Munck, J. P. Verbunt,
+F. Bijma, R. M. Heethaar, and F. Lopes da Silva, "In vivo measurement
+of the brain and skull resistivities using an EIT-based method and
+realistic models for the head," IEEE Trans Biomed Eng, vol. 50,
+pp. 754-67, 2003.
+
+S. Lew, C. H. Wolters, A. Anwander, S. Makeig, and R. S.
+MacLeod, "Improved EEG source analysis using low-resolution conductivity
+estimation in a four-compartment finite element head model," Hum
+Brain Mapp, vol. 30, pp. 2862-78, 2009.
+
+fMRI-weighted estimates
+#######################
+
+A. M. Dale, A. K. Liu, B. R. Fischl, R. L. Buckner, J. W.
+Belliveau, J. D. Lewine, and E. Halgren, "Dynamic statistical parametric
+mapping: combining fMRI and MEG for high-resolution imaging of cortical
+activity," Neuron, vol. 26, pp. 55-67, 2000.
+
+A. K. Liu, J. W. Belliveau, and A. M. Dale, "Spatiotemporal
+imaging of human brain activity using functional MRI constrained
+magnetoencephalography data: Monte Carlo simulations," Proc Natl
+Acad Sci U S A, vol. 95, pp. 8945-50., 1998.
+
+F. H. Lin, T. Witzel, M. S. Hamalainen, A. M. Dale, J. W.
+Belliveau, and S. M. Stufflebeam, "Spectral spatiotemporal imaging
+of cortical oscillations and interactions in the human brain," Neuroimage,
+vol. 23, pp. 582-95, 2004.
diff --git a/doc/source/manual/sampledata.rst b/doc/source/manual/sampledata.rst
new file mode 100644
index 0000000..b379fcd
--- /dev/null
+++ b/doc/source/manual/sampledata.rst
@@ -0,0 +1,769 @@
+
+
+.. _CHDDJDAA:
+
+===================
+The sample data set
+===================
+
+Purpose
+#######
+
+This Chapter gives a detailed description of the processing
+of a sample data set, which can be employed to familiarize with
+the workflow described in Chapter 3.
+
+.. note:: Going through the analysis exercise in this chapter is not a substitute for reading other chapters of this manual and understanding the concepts underlying MNE software.
+
+.. _CIHCDHGI:
+
+Overview
+########
+
+The MNE software is accompanied by a sample data set which
+includes the MRI reconstructions created with FreeSurfer and the
+an MEG/EEG data set. These data were acquired with the Neuromag
+Vectorview system at MGH/HMS/MIT Athinoula A. Martinos Center Biomedical
+Imaging. EEG data from a 60-channel electrode cap was acquired simultaneously with
+the MEG. The original MRI data set was acquired with a Siemens 1.5 T
+Sonata scanner using an MPRAGE sequence.
+
+.. note:: These data are provided solely for the purpose of getting familiar with the MNE software. They should not be redistributed to third parties. The data should not be used to evaluate the performance of the MEG or MRI system employed.
+
+In the MEG/EEG experiment, checkerboard patterns were presented
+into the left and right visual field, interspersed by tones to the
+left or right ear. The interval between the stimuli was 750 ms. Occasionally
+an smiley face was presented at the center of the visual field.
+The subject was asked to press a key with the right index finger
+as soon as possible after the appearance of the face. A listing
+of the corresponding trigger codes is provided in :ref:`BABDHIFJ`
+
+.. _BABDHIFJ:
+
+.. table:: Trigger codes for the sample data set.
+
+ ========= ===== ==========================================
+ Name #Contents
+ ========= ===== ==========================================
+ LA 1 Response to left-ear auditory stimulus
+ RA 2 Response to right-ear auditory stimulus
+ LV 3 Response to left visual field stimulus
+ RV 4 Response to right visual field stimulus
+ smiley 5 Response to the smiley face
+ button 32 Response triggered by the button press
+ ========= ===== ==========================================
+
+Setting up
+##########
+
+The sample data set is distributed with the MNE software
+as a compressed tar archive located at ``$MNE_ROOT/sample-data/MNE-sample-data.tar.gz`` .
+To make a personal copy of the sample data set, follow these steps:
+
+- Set up for using the MNE software as
+ instructed in Section 2.4 of this manual.
+
+- Create a directory for your personal copy: ``mkdir`` <yourdir> , where <yourdir> is
+ the location where you want your personal copy to reside. Tho store
+ the sample data set and to finish the tutorials in this Chapter, you
+ need approximately 600 MBytes of space on the disk where <yourdir> is
+ located.
+
+- Go to your newly created sample data directory: ``cd`` <yourdir> .
+
+- Extract the sample data: ``tar zxvf`` <dir> ``/MNE-sample-data.tar.gz`` ,
+ where <dir> is the location
+ of the tar archive, provided by your system administrator.
+
+To start the tutorials you need to:
+
+- Set up MNE software user environment,
+ see Section 2.4.
+
+- Set the SUBJECTS_DIR environment variable:``setenv SUBJECTS_DIR`` <yourdir> ``/subjects`` (csh
+ and tcsh) or ``export SUBJECTS_DIR=`` <yourdir> ``/subjects`` (POSIX-compatible
+ shell). Most users at the Martinos Center have tcsh as their login shell.
+
+- Assign the SUBJECT environment variable the value ``sample`` .
+
+- For convenience, you can also set the environment variable
+ SAMPLE to <yourdir> . The following
+ tutorial examples assume you have done this.
+
+- Set up the FreeSurfer environment
+ using the commands specific to your site. The FreeSurfer license
+ is needed for the source space creation covered in :ref:`CHDIGEJG`.
+
+.. note:: From this point on, directories and files under your personal copy of the sample data set under <yourdir> will be referred to by relative pathnames. For example, the file <yourdir> ``/MEG/sample/audvis.ave`` will be simply called ``MEG/sample/audvis.ave`` .
+
+.. note:: You can also proceed without FreeSurfer installed if you choose to use source space creation using the recursively subdivided octahedron or icosahedron method. For more information, see the Note in :ref:`CHDIGEJG`.
+
+Contents of the data set
+########################
+
+The sample data set contains two main directories: ``MEG/sample`` (the MEG/EEG
+data) and ``subjects/sample`` (the MRI reconstructions).
+An overview of the data provided is given in Tables :ref:`CHDDDIHE` and :ref:`CHDDEGGC`. In addition to
+subject sample , the MRI surface
+reconstructions from another subject, morph ,
+are provided to demonstrate the morphing capabilities of the MNE software.
+
+.. _CHDDDIHE:
+
+.. table:: Contents of the MEG/sample directory.
+
+ ======================== =====================================================================
+ File Contents
+ ======================== =====================================================================
+ sample/audvis_raw.fif The raw MEG/EEG data
+ audvis.ave A template script for off-line averaging
+ auvis.cov A template script for the computation of a noise-covariance matrix
+ ======================== =====================================================================
+
+.. _CHDDEGGC:
+
+.. table:: Overview of the contents of the subjects/sample directory.
+
+ ======================= ======================================================================
+ File / directory Contents
+ ======================= ======================================================================
+ bem Directory for the forward modelling data
+ bem/watershed BEM surface segmentation data computed with the watershed algorithm
+ bem/inner_skull.surf Inner skull surface for BEM
+ bem/outer_skull.surf Outer skull surface for BEM
+ bem/outer_skin.surf Skin surface for BEM
+ sample-head.fif Skin surface in fif format for mne_analyze visualizations
+ surf Surface reconstructions
+ mri/T1 The T1-weighted MRI data employed in visualizations
+ ======================= ======================================================================
+
+The following preprocessing steps have been already accomplished
+in the sample data set:
+
+- The MRI surface reconstructions have
+ been computed using the FreeSurfer software.
+
+- The BEM surfaces have been created with the watershed algorithm,
+ see Section A.1.
+
+- The MEG/EEG raw data file has been checked with the utilities described
+ in Sections 3.9.1 and 3.9.2.
+
+- Template scripts for averaging and computation of the noise-covariance
+ matrices have been written.
+
+Setting up subject-specific data
+################################
+
+.. _CHDBBAEJ:
+
+Structural MRIs
+===============
+
+To set up the structural MRIs for processing with the Neuromag
+MRI viewer, MRIlab, say
+
+``mne_setup_mri``
+
+This command sets up the directories ``subjects/sample/mri/T1-neuromag`` and ``subjects/sample/mri/brain-neuromag`` .
+For more information, see Section 3.4.
+
+.. _CHDIGEJG:
+
+Source space
+============
+
+The source space with a 5-mm grid spacing is set up by saying:
+
+``mne_setup_source_space --ico -6``
+
+This command sets up the source-space related files in directory ``subjects/sample/bem`` as
+described in Section 3.5.
+
+.. _CHDJDGBD:
+
+Boundary-element models
+=======================
+
+The geometry calculations for the single-layer boundary-element
+model are accomplished with the command:
+
+``mne_setup_forward_model --homog --surf --ico 4``
+
+This command sets up the homogeneous BEM-model related files
+in directory ``subjects/sample/bem`` as described in section Section 3.7. In
+addition to the homogeneous BEM, you also need the three-layer BEM model,
+which can be used for both EEG and MEG:
+
+``mne_setup_forward_model --surf --ico 4``
+
+The above commands employ the ``inner_skull.surf`` , ``outer_skull.surf`` ,
+and ``outer_skin.surf`` triangulation files located in ``subjects/sample/bem`` .
+The option ``--ico 4`` will create a model with 5120 triangles
+on each surface. Depending on the speed of your computer, the three-layer
+model may take quite a while to set up.
+
+Setting up a custom EEG layout
+##############################
+
+A data specific EEG layout will facilitate viewing of the
+EEG data. The MNE programs mne_browse_raw and mne_analyze look
+for user-specific layouts in ``$HOME/.mne/lout`` . Thus,
+you can create an EEG layout for the sample data set with the following
+commands:
+
+``mkdir -p $HOME/.mne/lout``
+
+``cd $SAMPLE/MEG/sample``
+
+``mne_make_eeg_layout --fif sample_audvis_raw.fif --lout $HOME/.mne/lout/sample-EEG.lout``
+
+Please refer to Section 11.6 for more information
+on mne_make_eeg_layout .
+
+.. note:: It is usually sufficient to create one EEG layout for each electrode cap you are using in your experiment rather than using a different layout file for each data file generated using the same cap.
+
+Previewing the data
+###################
+
+Previewing your raw data before proceeding to averaging and
+computation of the current estimates is most important to avoid
+unintentional errors caused by noisy or dysfunctional channels,
+frequent eye blinks, inappropriate bandpass filtering etc.
+
+One possible routemap for the preview session is outlined
+below:
+
+- Go to the MEG/EEG data directory: ``cd $SAMPLE/MEG/sample`` .
+
+- Launch mne_browse_raw .
+
+- Open the raw data file ``sample_audvis_raw.fif`` from File/Open... .
+
+- Switch all SSP vectors off from Adjust/Projection... .
+
+- Set the lowpass filter corner to a high value, e.g., 150 Hz
+ from Adjust/Filter... .
+
+- Browse through all channels using the selections available
+ under Adjust/Selection... and
+ look for very noisy or flat channels. You should be able to readily
+ identify two such channels among all MEG and EEG channels. You may
+ need to click Remove DC to reliably
+ associate the noisy or flat waveform with the channel name on the
+ left. Also, experiment with switching the EEG average reference
+ projection on and off and you will notice that the EEG bad channel
+ cannot be seen after the projection.
+
+- Mark the channels you identified in step 6. bad for this viewing
+ session by clicking on their channel names on the left. You can
+ save the bad channel selection to the file from File/Apply bad channels . Bad channel marking can be removed
+ by clicking on their channel names again and selecting File/Apply bad channels . Alternatively, you can use the utility mne_mark_bad_channels to
+ set a bad channel selection, see Section 11.4.1.
+
+- Switch the projections back on and change filter to a 40-Hz
+ lowpass.
+
+- Compute a preliminary average for the left-ear auditory stimulus:
+
+ - Open the averaging preferences dialog
+ (Adjust/Averaging preferences... .
+
+ - Set the time scale to -100...300 ms.
+
+ - Click on the text next to Average: in
+ the main window and press return. After a while, a topographical
+ display appears with the averaged responses. Notice that the bad
+ channels are not displayed.
+
+ - Change to different layouts from Adjust/Full view layout... . Inspect both the MEG and EEG waveforms.
+
+- Compute a preliminary average for the right-ear auditory stimulus:
+
+ - Open the averaging preferences.
+
+ - Click on the Trace color... button
+ and change the trace color to something different from the default
+ yellow.
+
+ - Change the text next to Average: to
+ 2 and press return. Average to the right-ear tones will be computed.
+ Compare the to sets of averages and verify that all channels show
+ reasonable data.
+
+- Go to Windows/Manage averages... and
+ delete the preliminary averages just computed.
+
+After these steps, you are ready to proceed to the actual
+analysis.
+
+Off-line averaging
+##################
+
+Go to directory ``$SAMPLE/MEG/sample`` . With help
+of Section 4.13, familiarize yourself with the averaging
+script ``audvis.ave`` .
+
+Using the averaging script interactively
+========================================
+
+You can invoke an averaging script in mne_browse_raw from Process/Average... .
+Select the ``audvis.ave`` script from the file selection
+box that appears. Once averaging is complete, you can inspect the
+details of the averaged responses in the Averages window,
+which appears automatically. You can redisplay it from Windows/Show averages... . The window, which appears when you
+select Adjust/Manage averages... allows
+you to:
+
+- Select which conditions (categories)
+ are displayed.
+
+- Change the trace colors.
+
+- Inspect the averaging log.
+
+- Save the averaged data.
+
+- Delete this set of averages.
+
+.. note:: If you decide to save the averages in the interactive mode, use the name ``sample_audvis-ave.fif`` for the result.
+
+Using the averaging script in batch mode
+========================================
+
+The batch-mode version of mne_browse_raw , mne_process_raw can
+be used for averaging as well. Batch mode averaging can be done
+with the command:
+
+``mne_process_raw --raw sample_audvis_raw.fif `` ``--lowpass 40 --projoff `` ``--saveavetag -ave --ave audvis.ave``
+
+The functions of the options are:
+
+**\---raw**
+
+ Specifies the raw file.
+
+**\---lowpass**
+
+ Specifies the lowpass filter corner frequency.
+
+**\---projoff**
+
+ Do not apply signal-space projection and average electrode reference
+ to the data. Regardless, the projection information is included with
+ the data file so that it can be applied later. It is also possible
+ to specify the ``--projon`` option but then there is no
+ possibility to view the original data in subsequent phases of the
+ analysis.
+
+**\---saveavetag**
+
+ Specifies how the averages are named. With this option, the ``_raw.fif`` ending
+ is stripped of the original raw data file and the tag specified
+ with this option (``-ave`` ) is added. The average file
+ and the corresponding log file will have the extensions ``.fif`` and ``.log`` , respectively.
+
+**\---ave**
+
+ Specifies the averaging script.
+
+As a result of running the averaging script a file called ``sample_audvis-ave.fif`` is
+created. It contains averages to the left and right ear auditory
+as well as to the left and right visual field stimuli.
+
+.. _CHDHBGGH:
+
+Viewing the off-line average
+############################
+
+The average file computed in the previous section can be
+viewed in mne_browse_raw .
+
+To view the averaged signals, invoke mne_browse_raw :
+
+``cd $SAMPLE/MEG/sample``
+
+``mne_browse_raw &``
+
+This Section gives only very basic information about the
+use of mne_browse_raw for viewing
+evoked-response data. Please consult Chapter 4 for more
+comprehensive information.
+
+Loading the averages
+====================
+
+mne_browse_raw loads all
+the available data from an average file at once:
+
+- Select Open evoked... from
+ the File menu.
+
+- Select the average file ``sample_audvis-ave.fif`` file
+ from the list and click OK .
+
+- A topographical display of the waveforms with gradiometer
+ channels included appears.
+
+Inspecting the auditory data
+============================
+
+Select the left and right ear auditory stimulus responses
+for display:
+
+- Select Manage averages... from
+ the Adjust menu.
+
+- Click off all other conditions except the auditory ones.
+
+Set the time scale and baseline:
+
+- Select Scales... from
+ the Adjust menu.
+
+- Switch off Autoscale time range and
+ set the Average time range from -200
+ to 500 ms.
+
+- Switch on Use average display baseline and
+ set Average display baseline from
+ -200 to 0 ms.
+
+- Click OK .
+
+You can display a subset of responses from the topographical display
+by holding the shift key down and dragging with the mouse, left
+button down. When you drag on the response with just the left button
+down, the signal timing, and channel name are displayed at the bottom. If
+the left mouse button is down and you press shift down the time
+is give both in absolute units and relative to the point where shift
+was pressed down.
+
+Observe the following:
+
+- The main deflection occurs around 100 ms
+ over the left and right temporal areas.
+
+- The left-ear response (shown in yellow) is stronger on the
+ right than on the left. The opposite is true for the right-ear response,
+ shown in red.
+
+Inspecting the visual data
+==========================
+
+Go back to the Manage averages... dialog
+and switch all other conditions except the visual ones.
+
+Observe the following:
+
+- The left and right visual field responses
+ are quite different in spatial distribution in the occipital area.
+
+- There is a later response in the right parietal area, almost
+ identical to both visual stimuli.
+
+.. note:: If you have the Neuromag software available, the averaged data can be also viewed in the Neuromag data plotter (xplotter ). See Section B.2 for instructions on how to use the Neuromag software at the MGH Martinos Center.
+
+Computing the noise-covariance matrix
+#####################################
+
+Another piece of information derived from the raw data file
+is the estimate for the noise-covariance matrix, which can be computed
+with the command:
+
+``mne_process_raw --raw sample_audvis_raw.fif `` ``--lowpass 40 --projon `` ``--savecovtag -cov --cov audvis.cov``
+
+Using the definitions in ``audvis.cov`` , this command
+will create the noise-covariance matrix file ``sample_audvis-cov.fif`` .
+In this case the projections are set on. The projection information
+is then attached to the noise-covariance matrix and will be automatically
+loaded when the inverse-operator decomposition is computed.
+
+.. note:: You can study the contents of the covariance matrix computation description file ``audvis.cov`` with help of Section 4.14
+
+.. _CHDIJBIG:
+
+MEG-MRI coordinate system alignment
+###################################
+
+The mne_analyze module
+of the MNE is one option for the coordinate alignment. It uses a
+triangulated scalp surface to facilitate the alignment.
+
+.. _CHDEDCAE:
+
+Initial alignment
+=================
+
+Follow these steps to make an initial approximation for the
+coordinate alignment.
+
+- Go to directory ``MEG/sample`` .
+
+- Launch mne_analyze
+
+- Select File/Load digitizer data... and
+ load the digitizer data from ``sample_audvis_raw.fif`` .
+
+- Load an inflated surface for subject sample from File/Load surface...
+
+- Bring up the viewer window from View/Show viewer...
+
+- Click Options... in the
+ viewer window. Make the following selections:
+
+ - Switch left and right cortical surface
+ display off.
+
+ - Make the scalp transparent.
+
+ - Switch Digitizer data on.
+
+- After a while, the digitizer points will be shown. The color
+ of the circles indicates whether the point is inside (blue) or outside
+ (red) of the scalp. The HPI coils are shown in green and the landmark
+ locations in light blue or light red color. The initial alignment
+ is way off!
+
+- Switch the Digitizer data off
+ to get the big circles out of the way.
+
+- Bring up the coordinate alignment window from Adjust/Coordinate alignment...
+
+- Click on the RAP (Right
+ Auricular Point) button. It turns red, indicating that you should
+ select the point from the viewer window. Click at the approximate
+ location of this point in the viewer. The button jumps up, turns
+ to normal color, and the MRI coordinates of the point appear in
+ the text fields next to the button.
+
+- Proceed similarly for the other two landmark points: Nasion
+ and LAP (Left Auricular Point).
+
+- Press Align using fiducials .
+ Notice that the coordinate transformation changes from a unit transformation
+ (no rotation, no origin translation) to a one determined by the
+ identified landmark locations. The rotation matrix (upper left 3
+ x 3 part of the transformation) should have positive values close
+ to one on the diagonal. Three is a significant rotation around the
+ x axis as indicated by elements (3,2) and (2,3) of the rotation
+ matrix. The *x* and *y* values
+ of the translation should be small and the *z* value
+ should be negative, around -50 mm. An example of an initial
+ coordinate transformation is shown in :ref:`CHDFIHAC`.
+
+- Make the Digitzer data again
+ visible from the options of the viewer window. Note that the points
+ are now much coloser to the scalp surface.
+
+.. _CHDFIHAC:
+
+.. figure:: picture.png
+ :alt: none
+
+ Example of an initial coordinate alignment.
+
+Refining the coordinate transformation
+======================================
+
+Before proceeding to the refinement procedure, it is useful
+to remove outlier digitizer points. When you rotate the image in
+the viewer window, you will notice that there is at least one such
+point over the right cheek. To discard this point:
+
+- Click on Discard in
+ the Adjust coordinate alignment window.
+
+- Enter 10 for the distance of the points to be discarded.
+
+- Click done. The outlier point disappears.
+
+The coordinate transformation can be adjusted manually with
+the arrow buttons in the middle part of the Adjust coordinate alignment dialog. These buttons move
+the digitizer points in the directions indicated by the amount listed
+next to each of the buttons.
+
+An automatic iterative procedure, Iterative Closest Point
+(ICP) matching is also provided. At each iteration step
+
+- For each digitizer point, transformed
+ from MEG to the MRI coordinate frame, the closest point on the triangulated
+ surface is determined.
+
+- The best coordinate transformation aligning the digitizer
+ points with the closest points on the head surface is computed.
+
+In step 2 of the iteration, the nasion is assigned five times
+the weight of the other points since it can be assumed that the
+nasion is the easiest point to identify reliably from the surface
+image.
+
+The ICP alignment can be invoked by entering the desired
+number of iterations next to the ICP align button
+followed by return or simply pressing the ICP align button.
+The iteration will converge in 10 to 20 steps.
+
+.. warning:: Use the ICP alignment option in mne_analyze with caution. The iteration will not converge to a reasonable solution unless and initial alignment is performed first according to :ref:`CHDEDCAE`. Outlier points should be excluded as described above. No attempt is made to compensate for the possible distance of the digitized EEG electrode locations from the scalp.
+
+Saving the transformation
+=========================
+
+To create a MRI fif description file which incorporates the
+coordinate transformation click Save MRI set in
+the Adjust coordinate alignment dialog.
+This will create the MRI set file in the ``$SUBJECTS_DIR/sample/mri/T1-neuromag/sets`` directory,
+which was created by mne_setup_mri_data ,
+see :ref:`CHDBBAEJ`. The file will be called
+
+``COR-`` <username>-<date>-<time> .fif
+
+where <username> is
+your login name.
+
+You can also save transformation to a fif file through the Save... button.
+If the file does not exist, it will only contain the coordinate
+transformation. If the file exists it will be inserted to the appropriate
+context. An existing transformation will not be replaced unless Overwrite existing transform is checked in the save dialog.
+
+Once you have saved the coordinate transformation, press Done and
+quit mne_analyze (File/Quit ).
+
+.. note:: If you dismiss the alignment dialog before saving the transformation, it will be lost.
+
+The forward solution
+####################
+
+To compute the forward solution, say:
+
+``cd $SAMPLE/MEG/sample``
+
+``mne_do_forward_solution --mindist 5 --spacing oct-6 --bem sample-5120-5120-5120 --meas sample_audvis-ave.fif``
+
+This produces an EEG and MEG forward solution with source
+space points closer than 5 mm to the inner skull surface omitted.
+The source space created in :ref:`CHDIGEJG` will be employed.
+As the output from this command will indicate The forward solution
+will be stored in file ``sample_audvis-ave-oct-6-fwd.fif`` .
+
+This command uses the three-layer BEM model ``sample-5120-5120-5120-bem-sol.fif`` created
+in :ref:`CHDJDGBD`. If you want to use the single-compartment
+BEM ``sample-5120-bem-sol.fif`` usable for MEG data only
+say:
+
+``cd $SAMPLE/MEG/sample``
+
+``mne_do_forward_solution --mindist 5 --spacing oct-6 --meas sample_audvis-ave.fif --bem sample-5120 --megonly``
+
+The inverse operator decomposition
+##################################
+
+The inverse operator information, necessary for the computation
+of the MNEs and dSPMs is accomplished by the command:
+
+``mne_do_inverse_operator --fwd sample_audvis-ave-oct-6-fwd.fif --depth --loose 0.2 --meg --eeg``
+
+This produces a depth-weighted inverse operator decomposition
+with 'loose' orientation constraint applied. More
+details on the convenience script mne_do_inverse_operator are
+provided in Section 3.13.
+
+The above command employs both EEG and MEG data. To create
+separate solution for EEG and MEG, run the commands:
+
+``mne_do_inverse_operator --fwd sample_audvis-ave-oct-6-fwd.fif --depth --loose 0.2 --meg``
+
+and
+
+``mne_do_inverse_operator --fwd sample_audvis-ave-oct-6-fwd.fif --depth --loose 0.2 --eeg``
+
+.. note:: If you were using a single-compartment BEM to compute the forward solution, you can only compute the MEG inverse operator.
+
+Interactive analysis
+####################
+
+The most exciting part of this exercise is to explore the
+data and the current estimates in mne_analyze .
+This section contains some useful steps to get you started. A lot
+of information about the capabilities of mne_analyze is
+given in Chapter 7. Batch-mode processing with mne_make_movie is discussed
+in Section 6.5. Cross-subject averaging is covered in Chapter 8.
+
+Before launching mne_analyze it
+is advisable to go to the directory ``MEG/sample`` . The
+current working directory can be also changed from mne_analyze .
+
+Getting started
+===============
+
+Launch mne_analyze . Select Help/On GLX... , which brings up a window containing Open
+GL rendering context information. If first line in the information
+dialog that pops up says Nondirect rendering context instead of Direct rendering context you will experience slow graphics
+performance. To fix this, your system software, graphics adapter
+or both need to be updated. Consult a computer support person for
+further information.
+
+Load surfaces
+=============
+
+It is reasonable to start the analysis by loading the display
+surfaces: choose the inflated surface for subject sample from
+the dialog that appears when you select File/Load surface... .
+
+Load the data
+=============
+
+Select File/Open... . Select ``sample_audvis-ave.fif`` as
+your data file and select the Left auditory data
+set. Select the inverse operator ``sample_audvis-ave-oct-6-meg-eeg-inv.fif`` and
+press OK . After a while the signals
+appear in the sample waveform and topographical displays. Click
+on the N100m peak in the auditory response. A dSPM map appears in
+the main surface display.
+
+Show field and potential maps
+=============================
+
+Select Windows/Show viewer... .
+After a while the viewer window appears. Click on the N100m peak
+again. Once the field map preparation computations are complete,
+the magnetic field and potential maps appear. Investigate the viewer
+window options with help of Section 7.10.
+
+Show current estimates
+======================
+
+The options affecting the current estimates are accessible
+from Adjust/Estimate parameters... .
+With help of Section 7.12, investigate the effects of the
+parameter settings.
+
+Labels and timecourses
+======================
+
+While in directory ``MEG/sample`` , create a directory
+called ``label`` :
+
+``mkdir label``
+
+Using the information in Section 7.13.4 create two
+labels: ``A-lh.label`` and ``A-rh.label`` in the
+approximate location of the left and right auditory cortices. Save
+these labels in the newly created ``label`` directory.
+
+Load all labels from the ``label`` directory and
+investigate the timecourses in these two labels as well as at invidual
+vertices. Information on label processing can be found from Section 7.13.
+
+Morphing
+========
+
+Goto to ``$SUBJECTS_DIR`` and create the directory ``morph-maps`` .
+Load the inflated surface for subject morph as
+the morphing surfaces. Try switching between the original and morphing
+surfaces. More information about morphing is available in Section 7.9 and
+in Chapter 8.
+
+There is also a left-hemisphere occipital patch file available
+for subject morph . Load a righ-hemifield
+visual response instead of the auditory one and investigate mapping
+of the current estimates on the patch.
diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst
new file mode 100644
index 0000000..a3ca7d0
--- /dev/null
+++ b/doc/source/manual/utilities.rst
@@ -0,0 +1,1362 @@
+
+
+.. _CHDBFDFG:
+
+=======================
+Miscellaneous utilities
+=======================
+
+Overview
+########
+
+This Chapter describes various utility programs included
+with the MNE software. Each utility documentation consists of a
+brief description of the purpose followed by the specification of
+command-line options.
+
+.. _CHDFIGBG:
+
+Finding software versions
+#########################
+
+The utility mne_list_versions lists
+version numbers and compilation dates of all software modules that
+provide this information. This administration utility is located
+in ``$MNE_ROOT/bin/admin`` , The output from mne_list_versions or
+output of individual modules with ``--version`` option
+is useful when bugs are reported to the developers of MNE software.
+
+.. _CHDHEDEF:
+
+Listing contents of a fif file
+##############################
+
+Using the utility mne_show_fiff it
+is possible to display information about the contents of a fif file
+to the standard output. The command line options for mne_show_fiff are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---in <name>**
+
+ Specifies the fif file whose contents will be listed.
+
+**\---verbose**
+
+ Produce a verbose output. The data of most tags is included in the output.
+ This excludes matrices and vectors. Only the first 80 characters
+ of strings are listed unless the ``--long`` option is present.
+
+**\---blocks**
+
+ Only list the blocks (the tree structure) of the file. The tags
+ within each block are not listed.
+
+**\---indent <number>**
+
+ Number of spaces for indentation for each deeper level in the tree structure
+ of the fif files. The default indentation is 3 spaces in terse and
+ no spaces in verbose listing mode.
+
+**\---long**
+
+ List all data from string tags instead of the first 80 characters.
+ This options has no effect unless the ``--verbose`` option
+ is also present.
+
+**\---tag <number>**
+
+ List only tags of this kind. Multiple ``--tag`` options
+ can be specified to list several different kinds of data.
+
+mne_show_fiff reads the
+explanations of tag kinds, block kinds, and units from ``$MNE_ROOT/share/mne/fiff_explanations.txt`` .
+
+Data file modification utilities
+################################
+
+This section contains utilities which can be used to add
+information or fix existing information in MEG/EEG data fif files.
+Unless otherwise noted these utilities can be applied to both raw
+and evoked data files.
+
+.. _CHDDHBEE:
+
+Designating bad channels: mne_mark_bad_channels
+===============================================
+
+This utility adds or replaces information about unusable
+(bad) channels. The command line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---bad <filename>**
+
+ Specify a text file containing the names of the bad channels, one channel
+ name per line. The names of the channels in this file must match
+ those in the data file exactly. If this option is missing, the bad channel
+ information is cleared.
+
+**<data file name>**
+
+ The remaining arguments are taken as data file names to be modified.
+
+.. _CHDBFDIC:
+
+Fixing the encoding of the trigger channel: mne_fix_stim14
+==========================================================
+
+Some earlier versions of the Neuromag acquisition software
+had a problem with the encoding of the eighth bit on the digital
+stimulus channel STI 014. This problem has been now fixed. Old data
+files can be fixed with mne_fix_stim14 ,
+which takes raw data file names as arguments. mne_fix_stim14 also
+changes the calibration of STI 014 to unity. If the encoding of
+STI 014 is already correct, running mne_fix_stim14 will
+not have any effect on the raw data.
+
+In newer Neuromag Vectorview systems with 16-bit digital
+inputs the upper two bytes of the samples may be incorrectly set
+when stimulus input 16 is used and the data are acquired in the
+32-bit mode. This problem can be fixed by running mne_fix_stim14 on
+a raw data file with the ``--32`` option:
+
+``mne_fix_stim14 --32`` <raw data file>
+
+In this case, the correction will be applied to the stimulus
+channels 'STI101' and 'STI201'.
+
+.. _CHDJGGGC:
+
+Updating EEG location info: mne_check_eeg_locations
+===================================================
+
+Some versions of the Neuromag acquisition software did not
+copy the EEG channel location information properly from the Polhemus
+digitizer information data block to the EEG channel information
+records if the number of EEG channels exceeds 60. The purpose of mne_check_eeg_locations is
+to detect this problem and fix it, if requested. The command-line
+options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---file <name>**
+
+ Specify the measurement data file to be checked or modified.
+
+**\---dig <name>**
+
+ Name of the file containing the Polhemus digitizer information. Default
+ is the data file name.
+
+**\---fix**
+
+ By default mne_check_eeg_locations only
+ checks for missing EEG locations (locations close to the origin).
+ With --fix mne_check_eeg_locations reads
+ the Polhemus data from the specified file and copies the EEG electrode
+ location information to the channel information records in the measurement
+ file. There is no harm running mne_check_eeg_locations on
+ a data file even if the EEG channel locations were correct in the
+ first place.
+
+.. _CHDGAAJC:
+
+Updating magnetometer coil types: mne_fix_mag_coil_types
+========================================================
+
+The purpose of mne_fix_mag_coil_types is
+to change coil type 3022 to 3024 in the MEG channel definition records
+in the data files specified on the command line.
+
+As shown in Tables 5.2 and 5.3, the Neuromag Vectorview systems
+can contain magnetometers with two different coil sizes (coil types
+3022 and 3023 vs. 3024). The systems incorporating coils of type
+3024 were introduced last. At some sites the data files have still
+defined the magnetometers to be of type 3022 to ensure compatibility
+with older versions of Neuromag software. In the MNE software as
+well as in the present version of Neuromag software coil type 3024
+is fully supported. Therefore, it is now safe to upgrade the data
+files to use the true coil type.
+
+If the ``--magnes`` option is specified, the 4D
+Magnes magnetometer coil type (4001) is changed to 4D Magnes gradiometer
+coil type (4002). Use this option always and *only
+if* your Magnes data comes from a system with axial gradiometers
+instead of magnetometers. The fif converter included with the Magnes
+system does not assign the gradiometer coil type correctly.
+
+.. note:: The effect of the difference between the coil sizes of magnetometer types 3022 and 3024 on the current estimates computed by the MNE software is very small. Therefore the use of mne_fix_mag_coil_types is not mandatory.
+
+.. _CHDCFEAJ:
+
+Modifying channel names and types: mne_rename_channels
+======================================================
+
+Sometimes it is necessary to change the names types of channels
+in MEG/EEG data files. Such situations include:
+
+- Designating an EEG as an EOG channel.
+ For example, the EOG channels are not recognized as such in the
+ fif files converted from CTF data files.
+
+- Changing the name of the digital trigger channel of interest
+ to STI 014 so that mne_browse_raw and mne_process_raw will
+ recognize the correct channel without the need to specify the --digtrig
+ option or the MNE_TRIGGER_CH_NAME environment variable every time a
+ data file is loaded.
+
+The utility mne_rename_channels was
+designed to meet the above needs. It recognizes the following command-line
+options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---fif <name>**
+
+ Specifies the name of the data file to modify.
+
+**\---alias <name>**
+
+ Specifies the text file which contains the modifications to be applied,
+ see below.
+
+**\---revert**
+
+ Reverse the roles of old and new channel names in the alias file.
+
+Each line in the alias file contains the old name and new
+name for a channel, separated by a colon. The old name is a name
+of one of the channels presently in the file and the new name is
+the name to be assigned to it. The old name must match an existing
+channel name in the file exactly. The new name may be followed by
+another colon and a number which is the channel type to be assigned
+to this channel. The channel type options are listed in :ref:`CHDFHGCA`.
+
+.. _CHDFHGCA:
+
+.. table:: Channel types.
+
+ ============== ======================
+ Channel type Corresponding number
+ ============== ======================
+ MEG 1
+ MCG 201
+ EEG 2
+ EOG 202
+ EMG 302
+ ECG 402
+ MISC 502
+ STIM 3
+ ============== ======================
+
+.. warning:: Do not attempt to designate MEG channels to EEG channels or vice versa. This may result in strange errors during source estimation.
+
+.. note:: You might consider renaming the EEG channels with descriptive labels related to the standard 10-20 system. This allows you to use standard EEG channel names when defining derivations, see Sections :ref:`CHDHJABJ` and 4.4.12, as well as in the channel selection files used in mne_browse_raw , see Section 4.5.5.
+
+.. _CHDBDDDF:
+
+Modifying trigger channel data: mne_add_triggers
+================================================
+
+Purpose
+-------
+
+The utility mne_add_triggers modifies
+the digital trigger channel (STI 014) in raw data files
+to include additional transitions. Since the raw data file is modified,
+it is possible to make irreversible changes. Use this utility with
+caution. It is recommended that you never run mne_add_triggers on
+an original raw data file.
+
+Command line options
+--------------------
+
+mne_add_triggers accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---raw <name>**
+
+ Specifies the raw data file to be modified.
+
+**\---trg <name>**
+
+ Specifies the trigger line modification list. This text file should
+ contain two entries per line: the sample number and the trigger
+ number to be added into the file. The number of the first sample
+ in the file is zero. It is recommended that trigger numbers whose
+ binary equivalent has lower eight bits equal to zero are used to
+ avoid conflicts with the ordinary triggers occurring in the file.
+
+**\---delete**
+
+ Delete the triggers defined by the trigger file instead of adding
+ them. This enables changing the file to its original state, provided
+ that the trigger file is preserved.
+
+.. note:: Since mne_browse_raw and mne_process_raw can employ an event file which effectively adds new trigger instants, mne_add_triggers is for the most part obsolete but it has been retained in the MNE software suite for backward compatibility.
+
+.. _CHDIJHIC:
+
+Removing identifying information
+================================
+
+Depending no the settings during acquisition in the Elekta-Neuromag EEG/MEG
+systems the data files may contain subject identifying information
+in unencrypted form. The utility mne_anonymize was
+written to clear tags containing such information from a fif file.
+Specifically, this utility removes the following tags from the fif
+file:
+
+.. _CHDEHBCG:
+
+.. table:: Tags cleared by mne_anonymize .
+
+ ======================== ==============================================
+ Tag Description
+ ======================== ==============================================
+ FIFF_SUBJ_FIRST_NAME First name of the subject
+ FIFF_SUBJ_MIDDLE_NAME Middle name of the subject
+ FIFF_SUBJ_LAST_NAME Last name of the subject
+ FIFF_SUBJ_BIRTH_DAY Birthday of the subject (Julian day number)
+ FIFF_SUBJ_SEX The sex of the subject
+ FIFF_SUBJ_HAND Handedness of the subject
+ FIFF_SUBJ_WEIGHT Weight of the subject in kg
+ FIFF_SUBJ_HEIGHT Height of the subject in m
+ FIFF_SUBJ_COMMENT Comment about the subject
+ ======================== ==============================================
+
+.. note:: mne_anonymize normally keeps the FIFF_SUBJ_HIS_ID tag which can be used to identify the subjects uniquely after the information listed in :ref:`CHDEHBCG` have been removed. If the --his option is specified on the command line, the FIFF_SUBJ_HIS_ID tag will be removed as well. The data of the tags listed in :ref:`CHDEHBCG` and the optional FIFF_SUBJ_HIS_ID tag are overwritten with zeros and the space claimed by omitting these tags is added to the free space [...]
+
+mne_anonymize recognizes
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---his**
+
+ Remove the FIFF_SUBJ_HIS_ID tag as well, see above.
+
+**\---file <name>**
+
+ Specifies the name of the file to be modified.
+
+.. note:: You need write permission to the file to be processed.
+
+.. _CJACECAH:
+
+Copying the processing history
+==============================
+
+In order for the inverse operator calculation to work correctly
+with data processed with the Elekta-Neuromag Maxfilter (TM) software,
+the so-called *processing history* block must
+be included in data files. Previous versions of the MNE Matlab functions
+did not copy processing history to files saved. As of March 30,
+2009, the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have
+been enchanced to include these data to the output file as appropriate.
+If you have older raw data files created in Matlab from input which
+has been processed Maxfilter, it is necessary to copy the *processing
+history* block from the original to modified raw data
+file using the mne_copy_processing_history utility described
+below. The raw data processing programs mne_browse_raw and mne_process_raw have
+handled copying of the processing history since revision 2.5 of
+the MNE software.
+
+mne_copy_processing_history is
+simple to use:
+
+``mne_copy_processing_history --from`` <from> ``--to`` <to> ,
+
+where <from> is an
+original raw data file containing the processing history and <to> is
+a file output with older MNE Matlab routines. Be careful: this operation
+cannot be undone. If the <from> file
+does not have the processing history block or the <to> file
+already has it, the destination file remains unchanged.
+
+.. _CHDHJABJ:
+
+Creating a derivation file
+##########################
+
+Purpose
+=======
+
+In mne_browse_raw , channel
+derivations are defined as linear combinations of real channels
+existing in the data files. The utility mne_make_derivations reads
+derivation data from a suitably formatted text file and produces
+a fif file containing the weights of derived channels as a sparse
+matrix. Two input file formats are accepted:
+
+- A file containing arithmetic expressions
+ defining the derivations and
+
+- A file containing a matrix which specifies the weights of
+ the channels in each derivation.
+
+Both of these formats are described in
+
+Command-line options
+====================
+
+mne_make_derivations recognizes
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---in <name>**
+
+ Specifies a measurement file which contains the EEG electrode locations.
+ This file is not modified.
+
+**\---inmat <name>**
+
+ Specifies the output file where the layout is stored. Suffix ``.lout`` is recommended
+ for layout files. mne_analyze and mne_browse_raw look
+ for the custom layout files from the directory ``$HOME/.mne/lout`` .
+
+**\---trans**
+
+ Indicates that the file specified with the ``--inmat`` option
+ contains a transpose of the derivation matrix.
+
+**\---thresh <value>**
+
+ Specifies the threshold between values to be considered zero and non-zero
+ in the input file specified with the ``--inmat`` option.
+ The default threshold is INLINE_EQUATION.
+
+**\---out <name>**
+
+ Specifies output fif file to contain the derivation data. The recommended
+ name of the derivation file has the format <name> ``-deriv.fif`` .
+
+**\---list <name>**
+
+ List the contents of a derivation file to standard output. If this
+ option is missing and ``--out`` is specified, the content
+ of the output file will be listed once it is complete. If neither ``--list`` nor ``--out`` is present,
+ and ``--in`` or ``--inmat`` is specified, the
+ interpreted contents of the input file is listed.
+
+Derivation file formats
+=======================
+
+All lines in the input files starting with the pound sign
+(#) are considered to be comments. The format of a derivation in
+a arithmetic input file is:
+
+<name> ``=`` [<INLINE_EQUATION>``*`` ]<INLINE_EQUATION > ``+`` \INLINE_EQUATION>``*`` ]<INLINE_EQUATION >INLINE_EQUATION
+
+where <name> is the
+name of the derived channel, INLINE_EQUATION are
+the names of the channels comprising the derivation, and INLINE_EQUATION are
+their weights. Note that spaces are necessary between the items.
+Channel names containing spaces must be put in quotes. For example,
+
+``EEG-diff = "EEG 003" - "EEG 002"``
+
+defines a channel ``EEG-diff`` which is a difference
+between ``EEG 003`` and ``EEG 002`` . Similarly,
+
+``EEG-der = 3 * "EEG 010" - 2 * "EEG 002"``
+
+defines a channel which is three times ``EEG 010`` minus
+two times ``EEG 002`` .
+
+The format of a matrix derivation file is:
+
+<nrow> <ncol> <names of the input channels>
+<INLINE_EQUATION> <weights> INLINE_EQUATION
+
+The combination of the two arithmetic examples, above can
+be thus represented as:
+
+``2 3 "EEG 002" "EEG 003" "EEG 010" EEG-diff -1 1 0 EEG-der -2 0 3``
+
+Before a derivation is accepted to use by mne_browse_raw ,
+the following criteria have to be met:
+
+- All channels to be combined into a single
+ derivation must have identical units of measure.
+
+- All channels in a single derivation have to be of the same
+ kind, *e.g.*, MEG channels or EEG channels.
+
+- All channels specified in a derivation have to be present
+ in the currently loaded data set.
+
+The validity check is done when a derivation file is loaded
+into mne_browse_raw , see Section 4.4.12.
+
+.. note:: You might consider renaming the EEG channels with descriptive labels related to the standard 10-20 system using the mne_rename_channels utility, see :ref:`CHDCFEAJ`. This allows you to use standard EEG channel names in the derivations you define as well as in the channel selection files used in mne_browse_raw , see Section 4.5.5.
+
+.. _CHDDGDJA:
+
+Creating a custom EEG layout
+############################
+
+Purpose
+=======
+
+Both MNE software (mne_analyze and mne_browse_raw )
+and Neuromag software (xplotter and xfit )
+employ text layout files to create topographical displays of MEG
+and EEG data. While the MEG channel layout is fixed, the EEG layout
+varies from experiment to experiment, depending on the number of
+electrodes used and the electrode cap configuration. The utility mne_make_eeg_layout was
+created to produce custom EEG layout files based on the EEG electrode
+location information included in the channel description records.
+
+mne_make_eeg_layout uses
+azimuthal equidistant projection to map the EEG channel locations
+onto a plane. The mapping consists of the following steps:
+
+- A sphere is fitted to the electrode
+ locations and the locations are translated by the location of the
+ origin of the best-fitting sphere.
+
+- The spherical coordinates (INLINE_EQUATION)
+ corresponding to each translated electrode location are computed.
+
+- The projected locations INLINE_EQUATION and INLINE_EQUATION are
+ computed. By default, INLINE_EQUATION, *i.e.* at
+ the equator (INLINE_EQUATION) the multiplier is
+ 20. This projection radius can be adjusted with the ``--prad`` option.
+ Increasing or decreasing INLINE_EQUATION makes
+ the spacing between the channel viewports larger or smaller, respectively.
+
+- A viewport with width 5 and height 4 is placed centered at
+ the projected location. The width and height of the viewport can
+ be adjusted with the ``--width`` and ``--height`` options
+
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---lout <name>**
+
+ Specifies the name of the layout file to be output.
+
+**\---nofit**
+
+ Do not fit a sphere to the electrode locations but use a standard sphere
+ center (INLINE_EQUATION, and INLINE_EQUATION instead.
+
+**\---prad <value>**
+
+ Specifies a non-standard projection radius INLINE_EQUATION,
+ see above.
+
+**\---width <value>**
+
+ Specifies the width of the viewports. Default value = 5.
+
+**\---height <value>**
+
+ Specifies the height of the viewports. Default value = 4.
+
+.. _BEHCBCGG:
+
+Adding neighborhood information to source spaces
+################################################
+
+Purpose
+=======
+
+The utility mne_add_patch_info uses
+the detailed cortical surface geometry information to add data about
+cortical patches corresponding to each source space point. A new
+copy of the source space(s) included in the input file is created
+with the patch information included. In addition to the patch information, mne_add_patch_info can
+optionally calculate distances, along the cortical surface, between
+the vertices selected to the source space.
+
+.. note:: Depending on the speed of your computer and the options selected, mne_add_patch_info takes 5 - 30 minutes to run.
+
+.. _CJAGCDCC:
+
+Command line options
+====================
+
+mne_add_patch_info accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---verbose**
+
+ Provide verbose output during the calculations.
+
+**\---dist <dist/mm>**
+
+ Invokes the calculation of distances between vertices included in
+ the source space along the cortical surface. Only pairs whose distance in
+ the three-dimensional volume is less than the specified distance are
+ considered. For details, see :ref:`CJAIFJDD`, below.
+
+**\---src <name>**
+
+ The input source space file. The source space files usually end
+ with ``-src.fif`` .
+
+**\---srcp <name>**
+
+ The output source space file which will contain the patch information.
+ If the file exists it will overwritten without asking for permission.
+ A recommended naming convention is to add the letter ``p`` after the
+ source spacing included in the file name. For example, if the input
+ file is ``mh-7-src.fif`` , a recommended output file name
+ is ``mh-7p-src.fif`` .
+
+**\---w <name>**
+
+ Name of a w file, which will contain the patch area information. Two
+ files will be created: <name> ``-lh.w`` and <name> ``-rh.w`` .
+ The numbers in the files are patch areas in INLINE_EQUATION.
+ The source space vertices are marked with value 150.
+
+**\---labeldir <directory>**
+
+ Create a label file corresponding to each of the patches in the
+ given directory. The directory must be created before running mne_add_patch_info .
+
+.. _CJAIFJDD:
+
+Computational details
+=====================
+
+By default, mne_add_patch_info creates
+a copy of the source space(s) with the following additional information
+for each vertex in the original dense triangulation of the cortex:
+
+- The number of the closest active source
+ space vertex and
+
+- The distance to this vertex.
+
+This information can be used to determine, *e.g.*,
+the sizes of the patches, their average normals, and the standard
+deviation of the normal directions. This information is also returned
+by the mne_read_source_space Matlab function as described in Table 10.28.
+
+The --dist option to mne_add_patch_info invokes
+the calculation of inter-vertex distances. These distances are computed
+along the the cortical surface (usually the white matter) on which
+the source space vertices are located.
+
+Since the calculation of all possible distances would take
+a very long time, the distance given with the --dist option allows
+restriction to the neighborhood of each source space vertex. This
+neighborhood is defined as the sphere around each source space vertex,
+with radius given by the --dist option. Because the distance calculation
+is done along the folded cortical surface whose details are given
+by the dense triangulation of the cortical surface produced by FreeSurfer,
+some of the distances computed will be larger than the value give
+with --dist.
+
+Converting covariance data into an SSP operator
+###############################################
+
+Purpose
+=======
+
+The utility mne_cov2proj picks
+eigenvectors from a covariance matrix and outputs them as a signal-space
+projection (SSP) file.
+
+Command line options
+====================
+
+mne_cov2proj accepts the
+following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---cov <name>**
+
+ The covariance matrix file to be used a source. The covariance matrix
+ files usually end with ``-cov.fif`` .
+
+**\---proj <name>**
+
+ The output file to contain the projection. It is recommended that
+ the file name ends with ``-proj.fif`` .
+
+**\---bad <name>**
+
+ Specify channels not to be included when an eigenvalue decomposition
+ of the covariance matrix is computed.
+
+**\---include <val1> [:<val2> ]**
+
+ Select an eigenvector or a range of eigenvectors to include. It
+ is recommended that magnetometers, gradiometers, and EEG data are handled
+ separately with help of the ``--bad`` , ``--meg`` , ``--megmag`` , ``--meggrad`` ,
+ and ``--eeg`` options.
+
+**\---meg**
+
+ After loading the covariance matrix, modify it so that only elements corresponding
+ to MEG channels are included.
+
+**\---eeg**
+
+ After loading the covariance matrix, modify it so that only elements corresponding
+ to EEG channels are included.
+
+**\---megmag**
+
+ After loading the covariance matrix, modify it so that only elements corresponding
+ to MEG magnetometer channels are included.
+
+**\---meggrad**
+
+ After loading the covariance matrix, modify it so that only elements corresponding
+ to MEG planar gradiometer channels are included.
+
+.. note:: The ``--megmag`` and ``--meggrad`` employ the Vectorview channel numbering scheme to recognize MEG magnetometers (channel names ending with '1') and planar gradiometers (other channels). Therefore, these options are only meaningful in conjunction with data acquired with a Neuromag Vectorview system.
+
+.. _CHDECHBF:
+
+Fitting a sphere to a surface
+#############################
+
+Purpose
+=======
+
+The utility mne_fit_sphere_to_surf finds
+the sphere which best fits a given surface.
+
+Command line options
+====================
+
+mne_fit_sphere_to_surf accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---bem <name>**
+
+ A BEM file to use. The names of these files usually end with ``bem.fif`` or ``bem-sol.fif`` .
+
+**\---surf <name>**
+
+ A FreeSurfer surface file to read. This is an alternative to using
+ a surface from the BEM file.
+
+**\---scalp**
+
+ Use the scalp surface instead of the inner skull surface in sphere
+ fitting. If the surface is specified with the ``--surf`` option,
+ this one is irrelevant.
+
+**\---mritrans <name>**
+
+ A file containing a transformation matrix between the MEG head coordinates
+ and MRI coordinates. With this option, the sphere origin will be
+ output in MEG head coordinates. Otherwise the output will be in MRI
+ coordinates.
+
+.. _CHDDCBGI:
+
+Computing sensitivity maps
+##########################
+
+Purpose
+=======
+
+mne_sensitivity_map computes
+the size of the columns of the forward operator and outputs the
+result in w files.
+
+Command line options
+====================
+
+mne_sensitivity_map accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---fwd <name>**
+
+ Specifies a forward solution file to analyze. By default the MEG
+ forward solution is considered.
+
+**\---proj <name>**
+
+ Specifies a file containing an SSP operator to be applied. If necessary,
+ multiple --proj options can be specified. For map types 1 - 4 (see
+ below), SSP is applied to the forward model data. For map types
+ 5 and 6, the effects of SSP are evaluated against the unmodified
+ forward model.
+
+**\---eeg**
+
+ Use the EEG forward solution instead of the MEG one. It does not make
+ sense to consider a combination because of the different units of
+ measure. For the same reason, gradiometers and magnetometers have
+ to be handled separately, see ``--mag`` option below. By
+ default MEG gradiometers are included.
+
+**\---mag**
+
+ Include MEG magnetometers instead of gradiometers
+
+**\---w <name>**
+
+ Specifies the stem of the output w files. To obtain the final output file
+ names, ``-lh.w`` and ``-rh.w`` is appended for
+ the left and right hemisphere, respectively.
+
+**\---smooth <number>**
+
+ Specifies the number of smooth steps to apply to the resulting w files.
+ Default: no smoothing.
+
+**\---map <number>**
+
+ Select the type of a sensitivity map to compute. At present, valid numbers
+ are 1 - 6. For details, see :ref:`CHDCDJIJ`, below.
+
+.. _CHDCDJIJ:
+
+Available sensitivity maps
+==========================
+
+In the following, let
+
+.. math:: 1 + 1 = 2
+
+denote the three consecutive columns of the gain matrix INLINE_EQUATION corresponding to
+the fields of three orthogonal dipoles at source space location INLINE_EQUATION.
+Further, lets assume that the source coordinate system has been
+selected so that the INLINE_EQUATION-axis points
+to the cortical normal direction and the INLINE_EQUATION plane
+is thus the tangent plane of the cortex at the source space location INLINE_EQUATION.
+Next, compute the SVD
+
+.. math:: 1 + 1 = 2
+
+and let INLINE_EQUATION, where INLINE_EQUATION and INLINE_EQUATION are
+the largest singular value and the corresponding left singular vector
+of INLINE_EQUATION, respectively. It is easy to see
+that INLINE_EQUATION is has the largest power
+among the signal distributions produced by unit dipoles at source
+space location INLINE_EQUATION.
+
+Furthermore, assume that the colums orthogonal matrix INLINE_EQUATION (INLINE_EQUATION) contain
+the orthogonal basis of the noise subspace corresponding to the signal
+space projection (SSP) operator INLINE_EQUATION specified
+with one or more ``--proj`` options so that INLINE_EQUATION.
+For more information on SSP, see Section 4.16.
+
+With these definitions the map selections defined with the ``--map`` option correspond
+to the following
+
+**\---map 1**
+
+ Compute INLINE_EQUATION at each source space point.
+ Normalize the result so that the maximum values equals one.
+
+**\---map 2**
+
+ Compute INLINE_EQUATION at each source space point.
+ Normalize the result so that the maximum values equals one. This
+ is the amplitude of the signals produced by unit dipoles normal
+ to the cortical surface.
+
+**\---map 3**
+
+ Compute INLINE_EQUATION at each source space point.
+
+**\---map 4**
+
+ Compute INLINE_EQUATION at each source space point.
+ This could be called the *radiality index*.
+
+**\---map 5**
+
+ Compute the subspace correlation between INLINE_EQUATION and INLINE_EQUATION: INLINE_EQUATION.
+ This index equals zero, if INLINE_EQUATION is
+ orthogonal to INLINE_EQUATION and one if INLINE_EQUATION lies
+ in the subspace defined by INLINE_EQUATION. This
+ map shows how close the field pattern of a dipole oriented perpendicular
+ to the cortex at each cortical location is to the subspace removed
+ by the SSP.
+
+**\---map 6**
+
+ Compute INLINE_EQUATION, which is the fraction
+ of the field pattern of a dipole oriented perpendicular to the cortex
+ at each cortical location remaining after applying the SSP a dipole
+ remaining
+
+.. _CHDDDJCA:
+
+Transforming locations
+######################
+
+Purpose
+=======
+
+mne_transform_points applies
+the coordinate transformation relating the MEG head coordinates
+and the MRI coordinates to a set of locations listed in a text file.
+
+Command line options
+====================
+
+mne_transform_points accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---in <name>**
+
+ Specifies the input file. The file must contain three numbers on
+ each line which are the *x*, *y*,
+ and *z* coordinates of point in space. By default,
+ the input is in millimeters.
+
+**\---iso <name>**
+
+ Specifies a name of a fif file containing Isotrak data. If this
+ option is present file will be used as the input instead of the
+ text file specified with the ``--in`` option.
+
+**\---trans <name>**
+
+ Specifies the name of a fif file containing the coordinate transformation
+ between the MEG head coordinates and MRI coordinates. If this file
+ is not present, the transformation will be replaced by a unit transform.
+
+**\---out <name>**
+
+ Specifies the output file. This file has the same format as the
+ input file.
+
+**\---hpts**
+
+ Output the data in the head points (hpts)
+ format accepted by tkmedit . In
+ this format, the coordinates are preceded by a point category (hpi,
+ cardinal or fiducial, eeg, extra) and a sequence number, see Section 9.3.1.
+
+**\---meters**
+
+ The coordinates are listed in meters rather than millimeters.
+
+**\---tomri**
+
+ By default, the coordinates are transformed from MRI coordinates to
+ MEG head coordinates. This option reverses the transformation to
+ be from MEG head coordinates to MRI coordinates.
+
+.. _CHDDIDCC:
+
+Inquiring and changing baselines
+################################
+
+The utility mne_change_baselines computes
+baseline values and applies them to an evoked-response data file.
+The command-line options are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---in <name>**
+
+ Specifies the input data file.
+
+**\---set <number>**
+
+ The data set number to compute baselines from or to apply baselines
+ to. If this option is omitted, all average data sets in the input file
+ are processed.
+
+**\---out <name>**
+
+ The output file.
+
+**\---baselines <name>**
+
+ Specifies a text file which contains the baseline values to be applied. Each
+ line should contain a channel name, colon, and the baseline value
+ given in 'native' units (T/m, T, or V). If this
+ option is encountered, the limits specified by previous ``--bmin`` and ``--bmax`` options will not
+ have an effect.
+
+**\---list <name>**
+
+ Specifies a text file to contain the baseline values. Listing is
+ provided only if a specific data set is selected with the ``--set`` option.
+
+**\---bmin <value/ms>**
+
+ Lower limit of the baseline. Effective only if ``--baselines`` option is
+ not present. Both ``--bmin`` and ``--bmax`` must
+ be present to compute the baseline values. If either ``--bmin`` or ``--bmax`` is
+ encountered, previous ``--baselines`` option will be ignored.
+
+**\---bmax <value/ms>**
+
+ Upper limit of the baseline.
+
+.. _CHDECAFD:
+
+Data simulator
+##############
+
+Purpose
+=======
+
+The utility mne_simu creates
+simulated evoked response data for investigation of the properties
+of the inverse solutions. It computes MEG signals generated by dipoles
+normal to the cortical mantle at one or several ROIs defined with
+label files. Colored noise can be added to the signals.
+
+Command-line options
+====================
+
+mne_simu has the following
+command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---fwd <name>**
+
+ Specify a forward solution file to employ in the simulation.
+
+**\---label <name>**
+
+ Specify a label
+
+**\---meg**
+
+ Provide MEG data in the output file.
+
+**\---eeg**
+
+ Provide EEG data in the output file.
+
+**\---out <name>**
+
+ Specify the output file. By default, this will be an evoked data
+ file in the fif format.
+
+**\---raw**
+
+ Output the data as a raw data fif file instead of an evoked one.
+
+**\---mat**
+
+ Produce Matlab output of the simulated fields instead of the fif evoked
+ file.
+
+**\---label <name>**
+
+ Define an ROI. Several label files can be present. By default, the sources
+ in the labels will have INLINE_EQUATION-shaped non-overlapping
+ timecourses, see below.
+
+**\---timecourse <name>**
+
+ Specifies a text file which contains an expression for a source
+ time course, see :ref:`CHDCFIBH`. If no --timecourse options
+ are present, the standard source time courses described in :ref:`CHDFIIII` are used. Otherwise, the time course expressions
+ are read from the files specified. The time course expressions are
+ associated with the labels in the order they are specified. If the
+ number of expressions is smaller than the number of labels, the
+ last expression specified will reused for the remaining labels.
+
+**\---sfreq <freq/Hz>**
+
+ Specifies the sampling frequency of the output data (default = 1000 Hz). This
+ option is used only with the time course files.
+
+**\---tmin <time/ms>**
+
+ Specifies the starting time of the data, used only with time course files
+ (default -200 ms).
+
+**\---tmax <time/ms>**
+
+ Specifies the ending time of the data, used only with time course files
+ (default 500 ms).
+
+**\---seed <number>**
+
+ Specifies the seed for random numbers. This seed is used both for adding
+ noise, see :ref:`CHDFBJIJ` and for random numbers in source waveform
+ expressions, see :ref:`CHDCFIBH`. If no seed is specified, the
+ current time in seconds since Epoch (January 1, 1970) is used.
+
+**\---all**
+
+ Activate all sources on the cortical surface uniformly. This overrides the ``--label`` options.
+
+.. _CHDFBJIJ:
+
+Noise simulation
+================
+
+Noise is added to the signals if the ``--senscov`` and ``--nave`` options
+are present. If ``--nave`` is omitted the number of averages
+is set to INLINE_EQUATION. The noise is computed
+by first generating vectors of Gaussian random numbers INLINE_EQUATION with INLINE_EQUATION.
+Thereafter, the noise-covariance matrix INLINE_EQUATIONis
+used to color the noise:
+
+.. math:: 1 + 1 = 2
+
+where we have used the eigenvalue decomposition positive-definite
+covariance matrix:
+
+.. math:: 1 + 1 = 2
+
+Note that it is assumed that the noise-covariance matrix
+is given for raw data, *i.e.*, for INLINE_EQUATION.
+
+.. _CHDFIIII:
+
+Simulated data
+==============
+
+The default source waveform INLINE_EQUATION for
+the INLINE_EQUATION label is nonzero at times INLINE_EQUATION, INLINE_EQUATION with:
+
+.. math:: 1 + 1 = 2
+
+i.e., the source waveforms are non-overlapping 100-samples
+wide INLINE_EQUATION pulses. The sampling frequency INLINE_EQUATION.
+The source amplitude INLINE_EQUATION is determined
+so that the strength of each of the dipoles in a label will be INLINE_EQUATION.
+
+Let us denote the sums of the magnetic fields and electric
+potentials produced by the dipoles normal to the cortical mantle
+at label INLINE_EQUATION **by INLINE_EQUATION. The simulated
+signals are then:
+
+.. math:: 1 + 1 = 2
+
+where INLINE_EQUATION is the number of
+sources.
+
+.. _CHDCFIBH:
+
+Source waveform expressions
+===========================
+
+The ``--timecourse`` option provides flexible possibilities
+to define the source waveforms in a functional form. The source
+waveform expression files consist of lines of the form:
+
+<variable> ``=`` <arithmetic expression>
+
+Each file may contain multiple lines. At the end of the evaluation,
+only the values in the variable ``y`` (``q`` )
+are significant, see :ref:`CHDJBIEE`. They assume the role
+of INLINE_EQUATION to compute the simulated signals
+as described in :ref:`CHDFIIII`, above.
+
+All expressions are case insensitive. The variables are vectors
+with the length equal to the number of samples in the responses,
+determined by the ``--tmin`` , ``--tmax`` , and ``--sfreq`` options.
+The available variables are listed in :ref:`CHDJBIEE`.
+
+.. _CHDJBIEE:
+
+.. table:: Available variable names in source waveform expressions.
+
+ ================ =======================================
+ Variable Meaning
+ ================ =======================================
+ x time\]
+ t current value of x in\s]
+ y the source amplitude\m]
+ q synonym for y
+ a , b , c , d help variables, initialized to zeros
+ ================ =======================================
+
+The arithmetic expressions can use usual arithmetic operations
+as well as mathematical functions listed in :ref:`CHDJIBHA`.
+The arguments can be vectors or scalar numbers. In addition, standard
+relational operators (<, >, ==, <=, >=) and their textual
+equivalents (lt, gt, eq, le, ge) are available. Table :ref:`CHDDJEHH` gives some useful examples of source waveform
+expressions.
+
+.. _CHDJIBHA:
+
+.. table:: Mathematical functions available for source waveform expressions
+
+ ================ ===============================================================================================================================================================================================================================
+ Function Description
+ ================ ===============================================================================================================================================================================================================================
+ abs(x) absolute value
+ acos(x) INLINE_EQUATION
+ asin(x) INLINE_EQUATION
+ atan(x) INLINE_EQUATION
+ atan2(x,y) INLINE_EQUATION
+ ceil(x) nearest integer larger than *x*
+ cos(x) INLINE_EQUATION
+ cosw(x,a,b,c) INLINE_EQUATION-shaped window centered at INLINE_EQUATION with a rising slope of length INLINE_EQUATION and a trailing slope of length INLINE_EQUATION.
+ deg(x) The value of INLINE_EQUATION converted to from radians to degrees
+ erf(x) INLINE_EQUATION
+ erfc(x) INLINE_EQUATION
+ exp(x) INLINE_EQUATION
+ floor(x) Largest integer value not larger than INLINE_EQUATION
+ hypot(x,y) INLINE_EQUATION
+ ln(x) INLINE_EQUATION
+ log(x) INLINE_EQUATION
+ maxp(x,y) Takes the maximum between INLINE_EQUATION and INLINE_EQUATION
+ minp(x,y) Takes the minimum between INLINE_EQUATION and INLINE_EQUATION
+ mod(x,y) Gives the remainder of INLINE_EQUATION divided by INLINE_EQUATION
+ pi Ratio of the circumference of a circle and its diameter.
+ rand Gives a vector of uniformly distributed random numbers from 0 to 1.
+ rnorm(x,y) Gives a vector of Gaussian random numbers distributed as INLINE_EQUATION. Note that if INLINE_EQUATION and INLINE_EQUATION are vectors, each number generated will a different mean and variance according to the arguments.
+ shift(x,s) Shifts the values in the input vector INLINE_EQUATION by the number of positions given by INLINE_EQUATION. Note that INLINE_EQUATION must be a scalar.
+ sin(x) INLINE_EQUATION
+ sqr(x) INLINE_EQUATION
+ sqrt(x) INLINE_EQUATION
+ tan(x) INLINE_EQUATION
+ ================ ===============================================================================================================================================================================================================================
+
+.. _CHDDJEHH:
+
+.. table:: Examples of source waveform expressions.
+
+ ============================================= =======================================================================================================================
+ Expression Meaning
+ ============================================= =======================================================================================================================
+ q = 20e-9*sin(2*pi*10*x) A 10-Hz sine wave with 20 nAm amplitude
+ q = 20e-9*sin(2*pi*2*x)*sin(2*pi*10*x) A 10-Hz 20-nAm sine wave, amplitude modulated sinusoidally at 2 Hz.
+ q = 20e-9*cosw(t,100,100,100) INLINE_EQUATION-shaped pulse, centered at INLINE_EQUATION with 100 ms leading and trailing slopes, 20 nAm amplitude.
+ q = 30e-9*(t > 0)*(t < 300)*sin(2*pi*20*x) 20-Hz sine wave, 30 nAm amplitude, cropped in time to 0...300 ms.
+ ============================================= =======================================================================================================================
+
+.. _CHDEDHCG:
+
+Converting parcellation data into labels
+########################################
+
+The utility mne_annot2labels converts
+cortical parcellation data into a set of labels. The parcellation
+data are read from the directory ``$SUBJECTS_DIR/$SUBJECT/label`` and
+the resulting labels are written to the current directory. mne_annot2labels requires
+that the environment variable ``$SUBJECTS_DIR`` is set.
+The command line options for mne_annot2labels are:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---subject <name>**
+
+ Specifies the name of the subject. If this option is not present
+ the ``$SUBJECT`` environment variable is consulted. If
+ the subject name cannot be determined, the program quits.
+
+**\---parc <name>**
+
+ Specifies the parcellation name to convert. The corresponding parcellation
+ file names will be ``$SUBJECTS_DIR/$SUBJECT/label/`` <hemi> ``h.`` <name> ``.annot`` where <hemi> is ``l`` or ``r`` for the
+ left and right hemisphere, respectively.
diff --git a/doc/source/tutorial.rst b/doc/source/tutorial.rst
index 1b406a6..9b6b3e7 100644
--- a/doc/source/tutorial.rst
+++ b/doc/source/tutorial.rst
@@ -1,8 +1,8 @@
.. _example_config:
-======================================
-Getting starting with MNE command line
-======================================
+=====================================
+Getting started with MNE command line
+=====================================
The quick start guide shows how to run a standard processing of the
sample data set provided with MNE. XXX add link to data set download
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