[med-svn] [python-mne] 109/376: starting manual editing of the manual
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:17 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 ab71920d96cb3fc81cb2821b23d56930c15236f9
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Thu Mar 3 14:50:07 2011 -0500
starting manual editing of the manual
---
doc/source/manual/analyze.rst | 176 +++++++-------
doc/source/manual/browse.rst | 90 ++++---
doc/source/manual/convert.rst | 32 +--
doc/source/manual/cookbook.rst | 65 ++---
doc/source/manual/forward.rst | 16 +-
doc/source/manual/index.rst | 2 +-
doc/source/manual/intro.rst | 6 +-
doc/source/manual/list.rst | 420 +++++++++++++++++++++++++--------
doc/source/manual/matlab.rst | 12 +-
doc/source/manual/mne.rst | 22 +-
doc/source/manual/morph.rst | 16 +-
doc/source/manual/pics/proj-off-on.png | Bin 542805 -> 147837 bytes
doc/source/manual/reading.rst | 2 +-
doc/source/manual/sampledata.rst | 18 +-
14 files changed, 564 insertions(+), 313 deletions(-)
diff --git a/doc/source/manual/analyze.rst b/doc/source/manual/analyze.rst
index a46fae4..e9c96ed 100644
--- a/doc/source/manual/analyze.rst
+++ b/doc/source/manual/analyze.rst
@@ -1,6 +1,6 @@
-.. _CACCICGI:
+.. _ch_interactive_analysis:
====================
Interactive analysis
@@ -138,10 +138,10 @@ The main window
.. _CACJABJI:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/main_window.png
+ :alt: main window of mne_analyze
- The main window of mne_analyze .
+ The main window of mne_analyze.
The main window of mne_analyze shown
in :ref:`CACJABJI` has the following components:
@@ -174,8 +174,8 @@ The File shown in :ref:`CACJCBFI` contains the following items:
.. _CACJCBFI:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/file_menu.png
+ :alt: the file menu
The File menu.
@@ -244,8 +244,8 @@ is shown in :ref:`CACFDIJJ`:
.. _CACFDIJJ:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/adjust_menu.png
+ :alt: The Adjust menu
The Adjust menu.
@@ -282,8 +282,8 @@ The contents of the file menu is shown in :ref:`CACBFCGF`:
.. _CACBFCGF:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/view_menu.png
+ :alt: The View menu
The View menu.
@@ -315,8 +315,8 @@ is discussed in detail in :ref:`CACCCFHH`.
.. _CACHCDCF:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/labels_menu.png
+ :alt: The Labels menu
The Labels menu.
@@ -357,8 +357,8 @@ The contents of the dipoles menu is shown in :ref:`CACCJDAF`:
.. _CACCJDAF:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/dipoles_menu.png
+ :alt: The dipole fitting menu
The dipole fitting menu.
@@ -382,8 +382,8 @@ is shown in :ref:`CACGFEAF`:
.. _CACGFEAF:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/help_menu.png
+ :alt: The Help menu
The Help menu.
@@ -454,8 +454,8 @@ dialog shown in :ref:`CACFHAIH` appears. It has four sections:
.. _CACFHAIH:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/open_dialog.png
+ :alt: The open dialog
The open dialog.
@@ -513,8 +513,8 @@ by the epoch selector show in :ref:`CACDCGIB`.
.. _CACDCGIB:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/epoch_selector.png
+ :alt: The raw data epoch selector
The raw data epoch selector.
@@ -700,8 +700,8 @@ shown in :ref:`CACJJCGD` has the following entries:
.. _CACJJCGD:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/scales_dialog.png
+ :alt: The Scales dialog
The Scales dialog.
@@ -748,8 +748,8 @@ shown in :ref:`CACDGJDC` appears.
.. _CACDGJDC:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/surface_selection_dialog.png
+ :alt: The surface selection dialog
The surface selection dialog.
@@ -797,8 +797,8 @@ hemisphere, rh = right hemisphere).
.. _CACHEEJD:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/patch_selection_dialog.png
+ :alt: patch selection dialog
The patch selection dialog.
@@ -838,8 +838,8 @@ The main surface display has a section called Adjust view , which has the contro
.. _CACCFCGJ:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/surface_controls.png
+ :alt: Surface controls
Surface controls.
@@ -1006,8 +1006,8 @@ using a color adjustment dialog accessible through the Color... buttons.
.. _CACDDHAI:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/adjust_lights.png
+ :alt: lighting adjustment dialog
The lighting adjustment dialog.
@@ -1018,8 +1018,8 @@ Producing output files
.. _CACFBIHD:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/hardcopy_controls.png
+ :alt: Graphics output controls
Graphics output controls.
@@ -1053,15 +1053,15 @@ surface display using the graphics output buttons shown in :ref:`CACFBIHD`:
.. _CACCEFGI:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/image_dialog.png
+ :alt: File type selection in the image saving dialog
File type selection in the image saving dialog.
.. _CACFFBBD:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/movie_dialog.png
+ :alt: The controls in the movie saving dialog
The controls in the movie saving dialog.
@@ -1130,7 +1130,7 @@ 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
+see :ref:`ch_morph`. 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`.
@@ -1152,8 +1152,8 @@ Overview
.. _CACJDFFH:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/viewer.png
+ :alt: viewer window
The viewer window with a visualization of MEG and EEG contour maps.
@@ -1268,8 +1268,8 @@ has the same effect on trackball operation.
Viewer options
==============
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/viewer_options.png
+ :alt: viewer options
The viewer options window
@@ -1481,8 +1481,8 @@ The parameters of the field maps can be adjusted from the Field mapping preferen
.. _CACGDCGA:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/field_mapping_pref.png
+ :alt: Field mapping preferences dialog
Field mapping preferences dialog.
@@ -1513,7 +1513,7 @@ and common sections:
**Number of smoothsteps**
- This option controls how much smoothing, see Section 8.3,
+ This option controls how much smoothing, see :ref:`CHDEBAHH`,
is applied to the interpolated data before computing the contours.
Usually the default value is appropriate.
@@ -1545,7 +1545,7 @@ controls:
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,
+ mismatch. Typical range of SNR values is 1...7. As discussed in :ref:`CBBDJFBJ`,
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
@@ -1587,22 +1587,36 @@ controls:
.. _CACGGICI:
+.. tabularcolumns:: |p{0.2\linewidth}|p{0.45\linewidth}|
.. 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.
- =========== =======================================================================================================================================================================================================================================================================================
+ +------------+---------------------------------------------------------+
+ | 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
+.. figure:: mne_analyze/MNE_preferences.png
+ :alt: MNE estimate preferences
Estimate preferences dialog.
@@ -1639,7 +1653,7 @@ The optional parameters are:
**# of smooth steps**
Before display, the data will be smoothed using this number of steps,
- see Section 8.3.
+ see :ref:`CHDEBAHH`.
**Opacity**
@@ -1665,7 +1679,7 @@ 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.
+operator, introduced in :ref:`CHDDHAGE`.
The computation of the apparent SNR will be explained in
future revisions of this manual.
@@ -1714,8 +1728,8 @@ stores the timecourse to the timecourse manager, :ref:`CACDIAAD`.
.. _CACJJGEF:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/label_list.png
+ :alt: label list
The label list.
@@ -1756,8 +1770,8 @@ the following controls for each timecourse stored:
.. _CACEDEJI:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/timecourse_manager.png
+ :alt: timecourse manager
The timecourse manager.
@@ -1796,8 +1810,8 @@ The vertex-by-vertex output formats is summarized in :ref:`CACEFHIJ`.
.. _CACHBBFD:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/save_label_timecourse.png
+ :alt: Label timecourse saving options
Label timecourse saving options.
@@ -1848,8 +1862,8 @@ Overlays
.. _CACIGHEJ:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/overlay_management.png
+ :alt: The overlay management dialog
The overlay management dialog.
@@ -1963,7 +1977,7 @@ 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.
+ MEG/EEG head coordinates, see :ref:`BJEBIBAI`.
**EEG scalp radius\m]**
@@ -2018,7 +2032,7 @@ of the dialog contains the following items:
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
+ discussed in more detail in :ref:`CBBHEGAB`. Especially if
EEG is included in fitting it is advisable to enter a non-zero value
(around 0.1) here.
@@ -2042,8 +2056,8 @@ of the dialog contains the following items:
.. _CACFEDEJ:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/dipole_parameters.png
+ :alt: The dipole fitting preferences dialog
The dipole fitting preferences dialog.
@@ -2133,8 +2147,8 @@ The dipole list
.. _CACGGFEJ:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/dipole_list.png
+ :alt: dipole list
The dipole list.
@@ -2270,8 +2284,8 @@ viewer window. To access the coordinate frame alignment tools:
- Bring up the Adjust coordinate alignment dialog from Adjust/Coordinate alignment... .
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/adjust_alignment.png
+ :alt: The coordinate frame alignment dialog
The coordinate frame alignment dialog.
@@ -2353,7 +2367,7 @@ 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.
+.. note:: One possible practical approach to coordinate frame alignment is discussed in :ref:`CHDIJBIG`.
.. _CHDCGHIF:
@@ -2433,8 +2447,8 @@ Viewing continuous HPI data
.. _CACFHFGJ:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/cont_hpi_data.png
+ :alt: Continuous HPI data overview
Continuous HPI data overview.
@@ -2513,8 +2527,8 @@ Working with the MRI viewer
.. _CHDEGEHE:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/mri_viewer.png
+ :alt: MRI viewer window
The MRI viewer control window.
@@ -2672,8 +2686,8 @@ an Elekta-Neuromag MEG system.
.. _CHDJJGII:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_analyze/visualize_hpi.png
+ :alt: Snapshot of mne_analyze in the head position visualization mode
Snapshot of mne_analyze in the head position visualization mode.
diff --git a/doc/source/manual/browse.rst b/doc/source/manual/browse.rst
index 64d6f5e..d8a7c7f 100644
--- a/doc/source/manual/browse.rst
+++ b/doc/source/manual/browse.rst
@@ -1,6 +1,6 @@
-.. _CACCICGI:
+.. _ch_browse:
===================
Processing raw data
@@ -15,7 +15,7 @@ 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
+with mne_analyze described in :ref:`ch_interactive_analysis` to
calculate current estimates from raw data interactively.
mne_browse_raw has also
@@ -408,8 +408,8 @@ These options apply to the batch-mode version, mne_process_raw only.
The user interface
##################
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/windows_menu-7.png
+ :alt: The user interface of mne_browse_raw
The user interface of mne_browse_raw
@@ -469,12 +469,12 @@ 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.
+.. 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 :ref:`ch_matlab`.
.. _CACBHGFE:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/open_dialog.png
+ :alt: Open dialog
The Open dialog.
@@ -576,7 +576,7 @@ 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
+in the MNE Matlab toolbox, see :ref:`ch_matlab`. For more information
on events, see :ref:`BABDFAHA`.
.. _CACFHAFH:
@@ -664,8 +664,8 @@ shown in :ref:`CACCEEGI`.
.. _CACCEEGI:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/filter_dialog.png
+ :alt: filter adjustment dialog
The filter adjustment dialog.
@@ -714,8 +714,8 @@ shown in :ref:`CACBJGBA`.
.. _CACBJGBA:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/scales_dialog.png
+ :alt: Scales dialog
The Scales dialog.
@@ -920,8 +920,8 @@ of this text file should be self explanatory.
.. _CACIHFFH:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/channel_selection.png
+ :alt: channel selection dialog
The channel selection dialog.
@@ -948,8 +948,8 @@ the modification of the selections:
.. _CACFECED:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/new_selection.png
+ :alt: Dialog to create a new channel selection
Dialog to create a new channel selection.
@@ -990,18 +990,28 @@ The components of the selection creation dialog shown in :ref:`CACFECED` have th
.. _CACHCHDJ:
+.. tabularcolumns:: |p{0.2\linewidth}|p{0.45\linewidth}|
.. 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.
- ==================== =================================================================================================
+ +--------------------+----------------------------------------------+
+ | 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.
@@ -1076,8 +1086,8 @@ Averaging preferences
.. _CACCFFAH:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/average_pref.png
+ :alt: Averaging preferences
Averaging preferences.
@@ -1208,8 +1218,8 @@ choice computes a new SSP operator as discussed in :ref:`BABFFCHF`.
.. _BABHAGHF:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/new_ssp.png
+ :alt: Time range specification for SSP operator calculation
Time range specification for SSP operator calculation
@@ -1333,8 +1343,8 @@ is shown in :ref:`CACGFEAF`:
.. _CACGFEAF:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/help_menu.png
+ :alt: Help menu
The Help menu.
@@ -1687,8 +1697,8 @@ The tool bar
.. _CACCFEGH:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/toolbar.png
+ :alt: tool bar controls
The tool bar controls.
@@ -2309,8 +2319,8 @@ of computed averages. The controls in the dialog, shown in :ref:`CACEFABD`, allo
.. _CACEFABD:
-.. figure:: picture.png
- :alt: none
+.. figure:: mne_browse_raw/manage_averages_dialog.png
+ :alt: dialog for managing available averages
The dialog for managing available averages.
@@ -2407,10 +2417,12 @@ please consult the references listed in Section 13.4.
.. _CACFGIEC:
-.. figure:: picture.png
- :alt: none
+.. figure:: pics/proj-off-on.png
+ :alt: example of the effect of SSP
- 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).
+ 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:
diff --git a/doc/source/manual/convert.rst b/doc/source/manual/convert.rst
index f698b74..3bd46db 100644
--- a/doc/source/manual/convert.rst
+++ b/doc/source/manual/convert.rst
@@ -1,6 +1,6 @@
-.. _BEHBBIJF:
+.. _ch_convert:
===============
Data conversion
@@ -446,7 +446,7 @@ To import the data, the following input files are mandatory:
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.
+.. note:: The output fif file will use the Neuromag head coordinate system convention, see :ref:`BJEBIBAI`. 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 :ref:`ch_matlab`.
The following input files are optional:
@@ -603,7 +603,7 @@ 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
+MNE software, see :ref:`BJEBIBAI`. 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.
@@ -642,7 +642,7 @@ The command-line options of mne_edf2fiff are:
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
+ see :ref:`ch_browse`. 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
@@ -790,7 +790,7 @@ 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.
+another format, see :ref:`ch_matlab`.
The command-line options of mne_brain_vision2fiff are:
@@ -851,7 +851,7 @@ 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 .
+It creates a BrainVision ``vhdr`` file and calls mne_brain_vision2fiff.
Usage:
``mne_eximia2fiff`` [--dig dfile ] [``--orignames`` ] file1 file2 ...
@@ -861,7 +861,7 @@ 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``
+``mne_eximia2fiff *.nxe``
The optional file specified with the --dig option is assumed
to contain digitizer data from the recording in the Nexstim format.
@@ -938,7 +938,7 @@ The command-line options of mne_convert_dig_data are:
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
+ see :ref:`BJEBIBAI`. 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
@@ -980,7 +980,7 @@ where
**<x/mm> , <y/mm> , <z/mm>**
- Location of the point, usually in the MEG head coordinate system, see Section 5.3.
+ Location of the point, usually in the MEG head coordinate system, see :ref:`BJEBIBAI`.
Some programs have options to accept coordinates in meters instead
of millimeters. With --meters option, mne_transform_points lists
the coordinates in meters.
@@ -1515,7 +1515,7 @@ 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.
+.. note:: Most of the functions of mne_convert_mne_data are now covered by the MNE Matlab toolbox covered in :ref:`ch_matlab`. This toolbox is recommended to avoid creating additional files occupying disk space.
.. _BEHCICCF:
@@ -1740,11 +1740,11 @@ The symbols employed in variable size descriptions are:
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
+ sing nchan The singular values of INLINE_EQUATION with INLINE_EQUATION selected so that INLINE_EQUATION as discussed in :ref:`CHDDHAGE`
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.
+ noise_eigenval nchan In terms of :ref:`CHDDHAGE`, eigenvalues of INLINE_EQUATION, i.e., not scaled with number of averages.
+ noise_eigenvec nchan Eigenvectors of the noise covariance matrix. In terms of :ref:`CHDDHAGE`, 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.
@@ -1762,7 +1762,7 @@ 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.
+.. note:: The MNE Matlab toolbox described in :ref:`ch_matlab` 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
====================
@@ -1870,7 +1870,7 @@ 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.
+.. note:: The MNE Matlab toolbox described in :ref:`ch_matlab` 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
====================
@@ -2087,4 +2087,4 @@ is provided in :ref:`BEHHAGHE`.
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`.
+.. note:: For source modelling purposes, it is recommended that the MNE Matlab toolbox, see :ref:`ch_matlab` 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
index 5255e27..de16ad8 100644
--- a/doc/source/manual/cookbook.rst
+++ b/doc/source/manual/cookbook.rst
@@ -1,6 +1,6 @@
-.. _CHDDJDAA:
+.. _ch_cookbook:
============
The Cookbook
@@ -15,10 +15,13 @@ is summarized in :ref:`CIHBIIAH`.
.. _CIHBIIAH:
-.. figure:: picture.png
- :alt: none
+.. figure:: pics/Flowchart.png
+ :alt: MNE Workflow Flowchart
+ :align: center
- Workflow of the MNE software. References in parenthesis indicate sections and chapters of this manual.
+ Workflow of the MNE software
+
+ References in parenthesis indicate sections and chapters of this manual.
Selecting the subject
#####################
@@ -49,7 +52,7 @@ 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.
+.. note:: Only the latest (4.0.X and later) FreeSurfer distributions contain a version of tkmedit which is compatible with mne_analyze, see :ref:`CACCHCBF`.
.. _BABCCEHF:
@@ -61,11 +64,11 @@ 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
+see :ref:`CACEHGCD`. 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.
+see :ref:`ch_matlab`.
These functions require running the script mne_setup_mri which
requires that the subject is set with the ``--subject`` option
@@ -87,7 +90,7 @@ 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.
+described in :ref:`BABBHHHE` to convert the data.
For example:
@@ -181,7 +184,7 @@ The script accepts the following options:
**\---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
+ are computed, see :ref:`CBBDBHDI`. 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
@@ -292,7 +295,7 @@ are:
.. 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:: The mne_convert_surface utility described in :ref:`BEHDIAJG` 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.
@@ -322,7 +325,7 @@ the forward solutions:
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
+0.006 S/m. Recent publications, see :ref:`CEGEGDEI`, 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
@@ -499,12 +502,12 @@ The following MEG and EEG data preprocessing steps are recommended:
- 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`
+- 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 information on these programs, please consult :ref:`ch_browse`.
- For evoked-response analysis, the data has to be re-averaged
off line, see :ref:`BABEAEDF`.
@@ -524,7 +527,7 @@ 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
+available in :ref:`CHDBFDIC`. 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.
@@ -555,7 +558,7 @@ 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
+see :ref:`CHDDHBEE`. 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
@@ -613,7 +616,7 @@ 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.
+be found in :ref:`ch_browse`.
.. _CHDBEHDC:
@@ -623,7 +626,7 @@ 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
+in :ref:`BJEBIBAI`. 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.
@@ -631,7 +634,7 @@ 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
+However, as explained in :ref:`BJEBIBAI`, 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
@@ -640,7 +643,7 @@ 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
+tools for coordinate frame alignment, see :ref:`ch_interactive_analysis`. :ref:`CHDIJBIG` also
contains tips for using mne_analyze for
this purpose.
@@ -649,7 +652,7 @@ 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
+data included in the measurement file as described in :ref:`BJEBIBAI`.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.
@@ -799,7 +802,7 @@ search sequence:
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
+see :ref:`CACEHGCD`. 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
@@ -856,7 +859,7 @@ ways:
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.
+from individual epochs. For details, see :ref:`ch_browse`.
.. _CIHCFJEI:
@@ -869,7 +872,7 @@ 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.
+computed. For mathematical details of this approach, please consult :ref:`CBBDJFBJ`.
This computation stage is facilitated by the convenience
script mne_do_inverse_operator . It
@@ -945,7 +948,7 @@ the following options:
**\---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.
+ Suitable values are in the range 0.05...0.2. For details, see :ref:`CBBHEGAB`.
**\---eegreg <value>**
@@ -962,14 +965,14 @@ the following options:
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)
+ a w file. It is recommended that this w file is appropriately smoothed (see :ref:`CHDEBAHH`)
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.
+ of the weighting is discussed in :ref:`CBBDIJHI`.
**\---fmrithresh <value>**
@@ -1025,7 +1028,7 @@ ways:
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.
+ please consult :ref:`ch_interactive_analysis`.
- The command-line tool mne_make_movie can
be invoked to produce QuickTime movies and snapshots. mne_make_movie can
@@ -1034,7 +1037,7 @@ ways:
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,
+ in :ref:`CBBECEDE`.
- The command-line tool mne_make_movie can
be employed to interrogate the source estimate waveforms from labels
@@ -1047,12 +1050,12 @@ ways:
- 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.
+ response MEG/EEG file, see :ref:`CBBCGHAH`.
- 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.
+ toolbox, see :ref:`ch_matlab`.
- It is also possible to average the source estimates across
- subjects as described in Chapter 8.
+ subjects as described in :ref:`ch_morph`.
diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst
index 9d65c57..e9a547a 100644
--- a/doc/source/manual/forward.rst
+++ b/doc/source/manual/forward.rst
@@ -1,6 +1,6 @@
-.. _CBBDEAAI:
+.. _ch_forward:
====================
The forward solution
@@ -29,10 +29,12 @@ to the front, and the INLINE_EQUATION axis up.
.. _CHDFFJIJ:
-.. figure:: picture.png
- :alt: none
+.. figure:: pics/CoordinateSystems.png
+ :alt: MEG/EEG and MRI coordinate systems
- 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.
+ 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:
@@ -161,8 +163,8 @@ and
The head and device coordinate systems
######################################
-.. figure:: picture.png
- :alt: none
+.. figure:: pics/HeadCS.png
+ :alt: Head coordinate system
The head coordinate system
@@ -1110,7 +1112,7 @@ 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
+methods described by Mosher, Zhang, and Berg, see :ref:`CEGEGDEI` (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:
diff --git a/doc/source/manual/index.rst b/doc/source/manual/index.rst
index d0c3498..c5ef4dc 100644
--- a/doc/source/manual/index.rst
+++ b/doc/source/manual/index.rst
@@ -11,7 +11,7 @@ MNE Manual
browse
forward
mne
- analyse
+ analyze
morph
convert
matlab
diff --git a/doc/source/manual/intro.rst b/doc/source/manual/intro.rst
index f81e389..39ef437 100644
--- a/doc/source/manual/intro.rst
+++ b/doc/source/manual/intro.rst
@@ -16,11 +16,11 @@ 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
+modules included with MNE software. :ref:`ch_cookbook` 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
+information about the software modules. :ref:`ch_sample_data` discusses
+processing of the sample data set included with the MNE software. :ref:`ch_reading` lists
some useful background material for the methods employed in the
MNE software.
diff --git a/doc/source/manual/list.rst b/doc/source/manual/list.rst
index ae173c0..ee22ad1 100644
--- a/doc/source/manual/list.rst
+++ b/doc/source/manual/list.rst
@@ -15,100 +15,306 @@ in italics. :ref:`BABDJHGH` lists various supplementary utilities.
.. _CHDDJIDB:
+.. tabularcolumns:: |p{0.3\linewidth}|p{0.65\linewidth}|
.. 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.
- ============================ ============================================================================================================================================================================================================================================================================================
+ +----------------------------+--------------------------------------------+
+ | Name | Purpose |
+ +============================+============================================+
+ | *mne_analyze* | An interactive analysis tool for computing |
+ | | source estimates, see |
+ | | :ref:`ch_interactive_analysis`. |
+ +----------------------------+--------------------------------------------+
+ | *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 :ref:`ch_browse`. |
+ +----------------------------+--------------------------------------------+
+ | *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 :ref:`CBBCGHAH`. |
+ +----------------------------+--------------------------------------------+
+ | *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 forwar |
+ | | 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 |
+ | | :ref:`CBBECEDE`. |
+ +----------------------------+--------------------------------------------+
+ | *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 :ref:`ch_browse`. |
+ +----------------------------+--------------------------------------------+
+ | 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:
+.. tabularcolumns:: |p{0.3\linewidth}|p{0.65\linewidth}|
.. 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.
- ================================== =========================================================================================================================================================================================
+ +---------------------------------+--------------------------------------------+
+ | 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 :ref:`BEHDIAJG`. |
+ +---------------------------------+--------------------------------------------+
+ | *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. |
+ +---------------------------------+--------------------------------------------+
+ | *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 :ref:`BABBHHHE`. |
+ +---------------------------------+--------------------------------------------+
+ | *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 :ref:`CHDDHBEE`. |
+ +---------------------------------+--------------------------------------------+
+ | *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
############
@@ -183,7 +389,8 @@ the three commands:
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 ,
+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:
@@ -193,7 +400,7 @@ For csh/tcsh the corresponding commands are:
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,
+from mne_analyze, see :ref:`CACCHCBF`,
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
@@ -204,17 +411,28 @@ listed in :ref:`CIHDGFAA`
.. _CIHDGFAA:
+.. tabularcolumns:: |p{0.3\linewidth}|p{0.55\linewidth}|
.. 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.
+ +-------------------------+--------------------------------------------+
+ | 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 :ref:`CACCHCBF`. |
+ +-------------------------+--------------------------------------------+
+ | 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
index f69f991..c9a7fee 100644
--- a/doc/source/manual/matlab.rst
+++ b/doc/source/manual/matlab.rst
@@ -1,6 +1,6 @@
-.. _CHDBFDFG:
+.. _ch_matlab:
==================
The Matlab toolbox
@@ -348,7 +348,7 @@ The documented structures are:
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
+ decomposition, see :ref:`CBBDJFBJ`. 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 [...]
@@ -693,9 +693,9 @@ The documented structures are:
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.
+ sing double(nchan) The singular values, *i.e.*, the diagonal values of INLINE_EQUATION, see :ref:`CHDBEHBC`.
+ eigen_leads double\nchan) The matrix INLINE_EQUATION, see :ref:`CHDBEHBC`.
+ eigen_fields double(nchan,nchan) The matrix INLINE_EQUATION, see :ref:`CHDBEHBC`.
noise_cov cov The noise covariance matrix C.
source_cov cov The source covariance matrix R.
src surf \ The description of the source spaces
@@ -704,7 +704,7 @@ The documented structures are:
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.
+ reginv double(nchan) The diagonal matrix INLINE_EQUATION, see :ref:`CHDBEHBC`.
noisenorm double\*) A sparse matrix containing the noise normalization factors. Dimension is either nsource (fixed source orientations) or 3*nsource (all source orientations).
=============== ====================== ==============================================================================================================================================================
diff --git a/doc/source/manual/mne.rst b/doc/source/manual/mne.rst
index 11b89a1..ed3b64d 100644
--- a/doc/source/manual/mne.rst
+++ b/doc/source/manual/mne.rst
@@ -1,6 +1,6 @@
-.. _CBBDEAAI:
+.. _ch_mne:
=====================
The current estimates
@@ -14,7 +14,7 @@ estimates. This is accomplished with two programs: *mne_inverse_operator* and *m
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.
+is covered in :ref:`ch_interactive_analysis`.
.. _CBBDJFBJ:
@@ -549,7 +549,7 @@ The command-line options of ``mne_inverse_operator`` are:
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
+ is appropriately smoothed (see :ref:`CHDEBAHH`) 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
@@ -640,9 +640,9 @@ 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.
+see :ref:`ch_interactive_analysis`, utilized in the cross-subject averaging
+process, see :ref:`ch_morph`, and read into Matlab using the MNE
+Matlab toolbox, see :ref:`ch_matlab`.
The command-line options to mne_make_movie are
explained in the following subsections.
@@ -813,7 +813,7 @@ Visualization options
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.
+ can be found in :ref:`ch_morph`.
**\---morphgrade <number>**
@@ -889,7 +889,7 @@ Visualization options
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.
+ see :ref:`CHDEBAHH`.
**\---nocomments**
@@ -1123,9 +1123,9 @@ 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,
+read to Matlab directly using the MNE Matlab Toolbox, see :ref:`ch_matlab`,
or converted to Matlab format using either mne_convert_mne_data , mne_raw2mat ,
-or mne_epochs2mat , see Chapter 9.
+or mne_epochs2mat , see :ref:`ch_convert`.
.. _CHDEIHFA:
@@ -1320,4 +1320,4 @@ 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.
+.. 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 :ref:`ch_matlab`. 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 :ref:`ch_ [...]
diff --git a/doc/source/manual/morph.rst b/doc/source/manual/morph.rst
index fb6ed01..082e22c 100644
--- a/doc/source/manual/morph.rst
+++ b/doc/source/manual/morph.rst
@@ -1,6 +1,6 @@
-.. _CACCICGI:
+.. _ch_morph:
======================
Morphing and averaging
@@ -229,7 +229,7 @@ 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.
+ use of the ``--morph`` option, see :ref:`CBBECEDE`.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
@@ -239,7 +239,7 @@ involves three straightforward steps:
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.
+ in :ref:`ch_matlab`.
- Use mne_analyze or mne_make_movie to
visualize the result or use the stc files from the previous step
@@ -247,10 +247,12 @@ involves three straightforward steps:
.. _CHDDJBDH:
-.. figure:: picture.png
- :alt: none
+.. figure:: pics/Averaging-flowchart.png
+ :alt: Workflow of the cross-subject averaging process in MNE
- Workflow of the cross-subject averaging process in MNE software. References in parenthesis indicate sections and chapters of this manual
+ Workflow of the cross-subject averaging process
+
+ 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.
@@ -404,4 +406,4 @@ 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.
+.. note:: It is straightforward to read and write stc files using the MNE Matlab toolbox described in :ref:`ch_matlab` and thus write custom Matlab functions to realize more complicated custom group analysis tools.
diff --git a/doc/source/manual/pics/proj-off-on.png b/doc/source/manual/pics/proj-off-on.png
index ec1f7d0..54e50f5 100644
Binary files a/doc/source/manual/pics/proj-off-on.png and b/doc/source/manual/pics/proj-off-on.png differ
diff --git a/doc/source/manual/reading.rst b/doc/source/manual/reading.rst
index 183f2b4..dc251b4 100644
--- a/doc/source/manual/reading.rst
+++ b/doc/source/manual/reading.rst
@@ -1,6 +1,6 @@
-.. _CACCICGI:
+.. _ch_reading:
==============
Useful reading
diff --git a/doc/source/manual/sampledata.rst b/doc/source/manual/sampledata.rst
index b379fcd..e3b37e4 100644
--- a/doc/source/manual/sampledata.rst
+++ b/doc/source/manual/sampledata.rst
@@ -1,6 +1,6 @@
-.. _CHDDJDAA:
+.. _ch_sample_data:
===================
The sample data set
@@ -11,7 +11,7 @@ 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.
+the workflow described in :ref:`ch_cookbook`.
.. 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.
@@ -259,7 +259,7 @@ below:
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.
+ set a bad channel selection, see :ref:`CHDDHBEE`.
- Switch the projections back on and change filter to a 40-Hz
lowpass.
@@ -387,7 +387,7 @@ To view the averaged signals, invoke 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
+evoked-response data. Please consult :ref:`ch_browse` for more
comprehensive information.
Loading the averages
@@ -558,8 +558,8 @@ coordinate alignment.
.. _CHDFIHAC:
-.. figure:: picture.png
- :alt: none
+.. figure:: pics/Digitizer-example.png
+ :alt: Example of an initial coordinate alignment
Example of an initial coordinate alignment.
@@ -685,8 +685,8 @@ 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.
+given in :ref:`ch_interactive_analysis`. Batch-mode processing with mne_make_movie is discussed
+in :ref:`CBBECEDE`. Cross-subject averaging is covered in :ref:`ch_morph`.
Before launching mne_analyze it
is advisable to go to the directory ``MEG/sample`` . The
@@ -761,7 +761,7 @@ 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.
+in :ref:`ch_morph`.
There is also a left-hemisphere occipital patch file available
for subject morph . Load a righ-hemifield
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