[med-svn] [python-mne] 160/376: DOC : adding appendices to manual
Yaroslav Halchenko
debian at onerussian.com
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yoh pushed a commit to annotated tag v0.1
in repository python-mne.
commit 551a07972b95c8145c0c9fd34ff3853dcd520e5d
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Thu Mar 24 16:25:28 2011 -0400
DOC : adding appendices to manual
---
doc/source/index.rst | 5 +
doc/source/manual/AppA.rst | 377 +++++++++++++++
doc/source/manual/AppB.rst | 294 ++++++++++++
doc/source/manual/AppEULA.rst | 133 ++++++
doc/source/manual/AppInstall.rst | 174 +++++++
doc/source/manual/AppReleaseNotes.rst | 877 ++++++++++++++++++++++++++++++++++
doc/source/manual/utilities.rst | 2 +-
7 files changed, 1861 insertions(+), 1 deletion(-)
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 56ac6f2..53355ab 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -29,6 +29,11 @@ Manual:
manual/utilities
manual/sampledata
manual/reading
+ manual/AppA
+ manual/AppB
+ manual/AppInstall
+ manual/AppReleaseNotes
+ manual/AppEULA
mne-python
* :ref:`search`
diff --git a/doc/source/manual/AppA.rst b/doc/source/manual/AppA.rst
new file mode 100644
index 0000000..d6cfda2
--- /dev/null
+++ b/doc/source/manual/AppA.rst
@@ -0,0 +1,377 @@
+
+
+.. _BGBDEIGC:
+
+=======================
+Creating the BEM meshes
+=======================
+
+.. _BABBDHAG:
+
+Using the watershed algorithm
+#############################
+
+The watershed algorithm\egonne *et al.*,
+2004] is part of the FreeSurfer software.
+The name of the program is mri_watershed .
+Its use in the MNE environment is facilitated by the script mne_watershed_bem ,
+which assumes the following options:
+
+**\---subject <subject>**
+
+ Defines the name of the subject. This can be also accomplished
+ by setting the SUBJECT environment variable.
+
+**\---overwrite**
+
+ Overwrite the results of previous run of mne_watershed_bem .
+
+**\---atlas**
+
+ Makes mri_watershed to employ
+ atlas information to correct the segmentation.
+
+After mne_watershed_bem has
+completed, the following files appear in the subject's ``bem/watershed`` directory:
+
+**<subject> _brain_surface**
+
+ Contains the brain surface triangulation.
+
+**<subject> _inner_skull_surface**
+
+ Contains the inner skull triangulation.
+
+**<subject> _outer_skull_surface**
+
+ Contains the outer skull triangulation.
+
+**<subject> _outer_skin_surface**
+
+ Contains the scalp triangulation.
+
+All of these surfaces are in the FreeSurfer format. In addition,
+there will be a directory called ``bem/watershed/ws`` which
+contains the brain MRI volume. Furthermore, mne_watershed_bem script
+converts the scalp surface to fif format and saves the result to ``bem/`` <subject> ``-head.fif`` . The mne_analyze tool
+described Chapter 7 looks for this file the visualizations
+involving the scalp surface.
+
+.. _BABFCDJH:
+
+Using FLASH images
+##################
+
+This method depends on the availablily of MRI data acquired
+with a multi-echo FLASH sequence at two flip angles (5 and 30 degrees).
+These data can be acquired separately from the MPRAGE data employed
+in FreeSurfer cortical reconstructions but it is strongly recommended
+that they are collected at the same time with the MPRAGEs or at
+least with the same scanner. For easy co-registration, the images
+should have FOV, matrix, slice thickness, gap, and slice orientation
+as the MPRAGE data. For information on suitable pulse sequences,
+see reference\. Fischl *et al.* and J. Jovicich *et
+al.*, 2006] in Section 13.3. At the Martinos
+Center, use of the 1.5-T Avanto scanner (Bay 2) is recommended for
+best results.
+
+Creation of the BEM meshes using this method involves the
+following steps:
+
+- Organizing the MRI data. This is facilitated
+ by the script mne_organize_dicom ,
+ see :ref:`BABEBJHI`.
+
+- Creating a synthetic 5-degree flip angle FLASH volume, register
+ it with the MPRAGE data, and run the segmentation and meshing program.
+ This step is accomplished by running the script mne_flash_bem , see :ref:`BABGICFE`.
+
+- Inspecting the meshes with tkmedit, see :ref:`BABHJBED`.
+
+.. note:: The following sections assume that you have run the appropriate setup scripts to make both MNE and FreeSurfer software available.
+
+.. _BABEBJHI:
+
+Organizing MRI data into directories
+====================================
+
+Since all images comprising the multi-echo FLASH data are
+contained in a single series, it is necessary to organize the images
+according to the echoes before proceeding to the BEM surface reconstruction.
+This is accomplished by the mne_organize_dicom script,
+which creates a directory tree with symbolic links to the original
+DICOM image files. To run mne_organize_dicom ,
+proceed as follows:
+
+- Copy all of your images or create symbolic
+ links to them in a single directory. The images must be in DICOM
+ format. We will refer to this directory as <source> .
+
+- Create another directory to hold the output of mne_organize_dicom . We
+ will refer to this directory as <dest> .
+
+- Change the working directory to <dest> .
+
+- Say ``mne_organize_dicom`` <source> .
+ Depending on the total number of images in <source> this
+ script may take quite a while to run. Progress is indicated by
+ listing the number of images processed at 50-image intervals.
+
+As a result, <dest> will
+contain several directories named <three-digit number> _<protocol_name> corresponding
+to the different series of images acquired. Spaces and parenthesis
+in protocol names will be replaced by underscores. Under each of
+these directories there are one or more directories named <three-digit> number
+corresponding to one or more subsets of images in this series (protocol).
+The only subset division scheme implemented in mne_organize_dicom is
+that according to different echoes, typically found in multi-echo
+FLASH data. These second level directories will contain symbolic
+links pointing to the original image data.
+
+.. note:: mne_organize_dicom was developed specifically for Siemens DICOM data. Its correct behavior with DICOM files originating from other MRI scanners has not been verified at this time.
+
+.. note:: Since mne_organize_dicom processes all images, not only the FLASH data, it may be a useful preprocessing step before FreeSurfer reconstruction process as well.
+
+.. _BABGICFE:
+
+Creating the surface tessellations
+==================================
+
+The BEM surface segmentation and tessellation is automated
+with the script mne_flash_bem .
+It assumes that a FreeSurfer reconstruction for this subject is
+already in place. The following options can be specified:
+
+**\---help**
+
+ Prints the usage information.
+
+**\---usage**
+
+ Prints the usage information.
+
+**\---noconvert**
+
+ Skip conversion of the original MRI data. The original data are
+ not needed and the preparatory steps 1.-3. listed below
+ are thus not needed.
+
+**\---noflash30**
+
+ The 30-degree flip angle data are not used.
+
+**\---unwarp <type>**
+
+ Run grad_unwarp with -unwarp <type> option on each of the converted
+ data sets.
+
+Before running mne_flash_bem do
+the following:
+
+- Run mne_organize_dicom as
+ described above.
+
+- Change to the <dest> directory
+ where mne_organize_dicom created the
+ image directory structure.
+
+- Create symbolic links from the directories containing the
+ 5-degree and 30-degree flip angle FLASH series to ``flash05`` and ``flash30`` , respectively:
+
+ - ``ln -s`` <FLASH 5 series dir> ``flash05``
+
+ - ``ln -s`` <FLASH 30 series dir> ``flash30``
+
+- Set the ``SUBJECTS_DIR`` and ``SUBJECT`` environment
+ variables
+
+.. note:: If mne_flash_bem is run with the --noflash30 option, the flash30 directory is not needed, *i.e.*, only the 5-degree flip angle flash data are employed.
+
+It may take a while for mne_flash_bem to
+complete. It uses the FreeSurfer directory structure under ``$SUBJECTS_DIR/$SUBJECT`` .
+The script encapsulates the following processing steps:
+
+- It creates an mgz file corresponding
+ to each of the eight echoes in each of the FLASH directories in ``mri/flash`` .
+ The files will be called ``mef`` <flip-angle> _<echo-number> ``.mgz`` .
+
+- If the --unwarp option is specified, run grad_unwarp and produce
+ files ``mef`` <flip-angle> _<echo-number> ``u.mgz`` .
+ These files will be then used in the following steps.
+
+- It creates parameter maps in ``mri/flash/parameter_maps`` using mri_ms_fitparms .
+
+- It creates a synthetic 5-degree flip angle volume in ``mri/flash/parameter_maps/flash5.mgz`` using mri_synthesize .
+
+- Using fsl_rigid_register ,
+ it creates a registered 5-degree flip angle volume ``mri/flash/parameter_maps/flash5_reg.mgz`` by
+ registering ``mri/flash/parameter_maps/flash5.mgz`` to
+ the *T1* volume under ``mri`` .
+
+- Using mri_convert , it converts
+ the flash5_reg volume to COR
+ format under ``mri/flash5`` . If necessary, the T1 and brain volumes
+ are also converted into the COR format.
+
+- It runs mri_make_bem_surfaces to
+ create the BEM surface tessellations.
+
+- It creates the directory ``bem/flash`` , moves the
+ tri-format tringulations there and creates the corresponding FreeSurfer
+ surface files in the same directory.
+
+- The COR format volumes created by mne_flash_bem are
+ removed.
+
+If the --noflash30 option is specified to mne_flash_bem ,
+steps 3 and 4 in the above are replaced by averaging over the different
+echo times in 5-degree flip angle data.
+
+.. _BABHJBED:
+
+Inspecting the meshes
+=====================
+
+It is advisable to check the validity of the BEM meshes before
+using them. This can be done with help of tkmedit either
+before or after executing mne_setup_forward_model ,
+see Section 3.7.
+
+Using seglab
+############
+
+The brain segmentation provided by FreeSurfer in the directory ``mri/brain`` can
+be employed to create the inner skull surface triangulation with
+help of seglab, the Neuromag MRI segmentation tool. The description
+below assumes that the user is familiar with the seglab tool. If
+necessary, consult the seglab manual, Neuromag P/N NM20420A-A.
+
+The data set mri/brain typically
+contains tissues within or outside the skull, in particular around
+the eyes. These must be removed manually before the inner skull
+triangulation is created.The editing and triangulation can be accomplished
+as outlined below
+
+**1. Set up the MRIs for Neuromag software access**
+
+ Run the mne_setup_mri too as described in Section 3.4.
+ As a result, the directories mri/T1-neuromag and mri/brain-neuromag
+ are set up.
+
+**2. Load the MRI data**
+
+ Open the file mri/brain-neuromag/sets/COR.fif and adjust the scaling
+ of the data.
+
+**3. Preparatory steps**
+
+ Set the minimum data value to 1 using the min3D operator.
+ Make a backup of the data with the backup3D operator.
+
+**4. Manual editing**
+
+ The maskDraw3D operation is recommended
+ for manual editing. To use it, first employ the grow3D operator
+ with threshold interval 2...255 and the seed point inside
+ the brain. Then do the editing in the slicer window as described
+ in Section 5.4.2 of the seglab manual. Note that it is enough to
+ remove the connectivity to the extracerebral tissues rather than
+ erasing them completely.
+
+**5. Grow again and mask**
+
+ Once manual editing is complete, employ the grow3D operator again
+ and do mask3D with the backup
+ data to see whether the result is satisfactory. If not, undo mask3D and
+ continue manual editing. Otherwise, undo mask3D and
+ proceed to the next step.
+
+**6. Dilation**
+
+ It is advisable to make the inner skull surface slightly bigger
+ than the brain envelope obtained in the previous step. Therefore,
+ apply the dilate3D operation
+ once or twice. Use the values 1 for nbours and 26 for nhood in the
+ first dilation and 1 and 18 in the second one, respectively.
+
+**7. Triangulation**
+
+ Triangulate the resulting object with the triangulate3D operator. Use
+ a sidelength of 5 to 6 mm. Check that the triangulation looks reasonable
+ in the 3D viewing window.
+
+**8. Save the triangulation**
+
+ Save the triangulated surface as a mesh into bem/inner_skull.tri. Select
+ unit of measure as millimeters and employ the MRI coordinate system.
+
+Using BrainSuite
+################
+
+The BrainSuite software
+running under the Windows operating system can also be used for
+BEM mesh generation. This software, written by David W. Shattuck,
+is distributed as a collaborative project between the Laboratory
+of Neuro Imaging at the University of California Los Angeles (Director:
+Dr. Arthur W. Toga) and the Biomedical Imaging Research Group at
+the University of Southern California (Director: Dr. Richard M. Leahy).
+For further information, see http://brainsuite.usc.edu/.
+
+The conversion of BrainSuite tessellation
+files to MNE software compatible formats is accomplished with the mne_convert_surface utility,
+covered in Section 9.7.
+
+The workflow needed to employ the BrainSuite tessellations
+is:
+
+**Step 1**
+
+ Using the mri_convert utility
+ available in FreeSurfer , convert
+ an MRI volume to the img (Analyze) format. This volume should be the
+ T1.mgz volume or a volume registered with T1.mgz in FreeSurfer :``mri_convert`` <volume> ``.mgz`` <volume> ``.img``
+
+**Step 2**
+
+ Transfer <volume> ``.mgz`` to
+ a location accessible to BrainSuite , running
+ on Windows.
+
+**Step 3**
+
+ Using <volume> ``.img`` as
+ input, create the tessellations of scalp, outer skull, and inner
+ skull surfaces in BrainSuite .
+
+**Step 4**
+
+ Transfer the dfs files containing the tessellations in the bem directory
+ of your subject's FreeSurfer reconstruction.
+
+**Step 5**
+
+ Go to the bem directory where you placed the two dfs files. Using mne_convert_surface ,
+ convert them to the FreeSurfer surface
+ format, *e,g.*:
+ ``mne_convert_surface `` ``--dfs inner_skull.dfs `` ``--mghmri ../mri/T1.mgz `` ``--surf inner_skull_dfs.surf``
+
+**Step 6**
+
+ Using tkmedit, check that the surfaces are correct, *e.g.*:
+ ``tkmedit -f ../mri/T1.mgz `` ``-surface inner_skull_dfs.surf``
+
+**Step7**
+
+ Using the mne_reduce_surface function
+ in Matlab, reduce the number of triangles on the surfaces to 10000
+ - 20000. Call the output files ``outer_skin.surf`` , ``outer_skull.surf`` ,
+ and ``inner_skull.surf`` .
+
+**Step 8**
+
+ Proceed to mne_setup_forward_model .
+ Use the ``--surf`` and ``--noswap`` options.
+
+.. note:: If left and right are flipped in BrainSuite, use the --flip option in mne_convert_surface to set the coordinate transformation correctly.
+
+.. note:: The BrainSuite scalp surface can be also used for visualization in mne_analyze , see Section 7.16.1.
diff --git a/doc/source/manual/AppB.rst b/doc/source/manual/AppB.rst
new file mode 100644
index 0000000..42c120f
--- /dev/null
+++ b/doc/source/manual/AppB.rst
@@ -0,0 +1,294 @@
+
+
+.. _BGBDEIGC:
+
+============================
+Setup at the Martinos Center
+============================
+
+This Appendix contains information specific to the Martinos
+Center setup.
+
+.. _CIHCDHGI:
+
+User environment
+################
+
+In the Martinos Center computer network, the 2.7 version
+of MNE is located at /usr/pubsw/packages/mne/stable. To use this
+version, follow Section 2.4 substituting /usr/pubsw/packages/mne/stable
+for <MNE> and /usr/pubsw/packages/matlab/current
+for <Matlab> . For most users,
+the default shell is tcsh.
+
+.. note:: A new version of MNE is build every night from the latest sources. This version is located at /usr/pubsw/packages/mne/nightly.
+
+.. _BABGFDJG:
+
+Using Neuromag software
+#######################
+
+Software overview
+=================
+
+The complete set of Neuromag software is available on the
+LINUX workstations. The programs can be accessed from the command
+line, see :ref:`BABFIEHC`. The corresponding manuals, located
+at ``$NEUROMAG_ROOT/manuals`` are listed in :ref:`BABCJJGF`.
+
+.. _BABFIEHC:
+
+.. table:: Principal Neuromag software modules.
+
+ =========== =================================
+ Module Description
+ =========== =================================
+ xfit Source modelling
+ xplotter Data plotting
+ graph General purpose data processor
+ mrilab MEG-MRI integration
+ seglab MRI segmentation
+ cliplab Graphics clipboard
+ =========== =================================
+
+.. _BABCJJGF:
+
+.. table:: List of Neuromag software manuals.
+
+ =========== =========================================
+ Module pdf
+ =========== =========================================
+ xfit XFit.pdf
+ xplotter Xplotter.pdf
+ graph GraphUsersGuide.pdf GraphReference.pdf
+ mrilab Mrilab.pdf
+ seglab Seglab.pdf
+ cliplab Cliplab.pdf
+ =========== =========================================
+
+To access the Neuromag software on the LINUX workstations
+in the Martinos Center, say (in tcsh or csh)
+
+``source /space/orsay/8/megdev/Neuromag-LINUX/neuromag_setup_csh``
+
+or in POSIX shell
+
+``. /space/orsay/8/megdev/Neuromag-LINUX/neuromag_setup_sh``
+
+Using MRIlab for coordinate system alignment
+============================================
+
+The MEG-MRI coordinate system alignment can be also accomplished with
+the Neuromag tool MRIlab, part of the standard software on Neuromag
+MEG systems.
+
+In MRIlab, the following steps are necessary for the coordinate
+system alignment:
+
+- Load the MRI description file ``COR.fif`` from ``subjects/sample/mri/T1-neuromag/sets`` through File/Open .
+
+- Open the landmark setting dialog from Windows/Landmarks .
+
+- Click on one of the coordinate setting fields on the Nasion line.
+ Click Goto . Select the crosshair
+ tool and move the crosshair to the nasion. Click Get .
+
+- Proceed similarly for the left and right auricular points.
+ Your instructor will help you with the selection of the correct
+ points.
+
+- Click OK to set the alignment
+
+- Load the digitization data from the file ``sample_audvis_raw.fif`` or ``sample_audvis-ave.fif`` (the
+ on-line evoked-response average file) in ``MEG/sample`` through File/Import/Isotrak data . Click Make points to
+ show all the digitization data on the MRI slices.
+
+- Check that the alignment is correct by looking at the locations
+ of the digitized points are reasonable. Adjust the landmark locations
+ using the Landmarks dialog, if
+ necessary.
+
+- Save the aligned file to the file suggested in the dialog
+ coming up from File/Save .
+
+Mature software
+###############
+
+This Section contains documentation for software components,
+which are still available in the MNE software but have been replaced
+by new programs.
+
+.. _BABDABHI:
+
+mne_compute_mne
+===============
+
+This chapter contains information about the options accepted
+by the program mne_compute_mne ,
+which is gradually becoming obsolete. All of its functions will
+be eventually included to mne_make_movie ,
+see Section 6.5. At this time, mne_compute_mne is
+still needed to produce time-collapsed w files unless you are willing
+to write a Matlab script of your own for this purpose.
+
+mne_compute_mne accepts
+the following command-line options:
+
+**\---version**
+
+ Show the program version and compilation date.
+
+**\---help**
+
+ List the command-line options.
+
+**\---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. The list of data sets can
+ be seen, *e.g.*, in mne_analyze , mne_browse_raw ,
+ and xplotter .
+
+**\---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.
+
+**\---nave <value>**
+
+ Specifies the number of averaged epochs in the input data. If the input
+ data file is one produced by mne_process_raw or mne_browse_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. This is accomplished
+ either by employing this flag or by adjusting the number of averages
+ in the data file with help of mne_change_nave .
+
+**\---snr <value>**
+
+ An estimate for the amplitude SNR. The regularization parameter will
+ be set as INLINE_EQUATION. If the SNR option is
+ absent, the regularization parameter will be estimated from the
+ data. The regularization parameter will be then time dependent.
+
+**\---snronly**
+
+ Only estimate SNR and output the result into a file called SNR. Each
+ line of the file contains three values: the time point in ms, the estimated
+ SNR + 1, and the regularization parameter estimated from the data
+ at this time point.
+
+**\---abs**
+
+ Calculate the absolute value of the current and the dSPM for fixed-orientation
+ data.
+
+**\---spm**
+
+ Calculate the dSPM instead of the expected current value.
+
+**\---chi2**
+
+ Calculate an approximate INLINE_EQUATION statistic
+ instead of the *F* statistic. This is simply
+ accomplished by multiplying the *F* statistic
+ by three.
+
+**\---sqrtF**
+
+ Take the square root of the INLINE_EQUATION or *F* statistic
+ before outputting the stc file.
+
+**\---collapse**
+
+ Make all frames in the stc file (or the wfile) identical. The value
+ at each source location is the maximum value of the output quantity
+ at this location over the analysis period. This option is convenient
+ for determining the correct thresholds for the rendering of the
+ final brain-activity movies.
+
+**\---collapse1**
+
+ Make all frames in the stc file (or the wfile) indentical. The value
+ at each source location is the INLINE_EQUATION norm
+ of the output quantity at this location over the analysis period.
+
+**\---collapse2**
+
+ Make all frames in the stc file (or the wfile) identical. The value
+ at each source location is the INLINE_EQUATION norm
+ of the output quantity at this location over the analysis period.
+
+**\---SIcurrents**
+
+ Output true current values in SI units (Am). By default, the currents are
+ scaled so that the maximum current value is set to 50 (Am).
+
+**\---out <name>**
+
+ Specifies the output file name. This is the 'stem' of
+ the output file name. The actual name is derived by removing anything up
+ to and including the last period from the end of <name> .
+ According to the hemisphere, ``-lh`` or ``-rh`` is
+ then appended. Finally, ``.stc`` or ``.w`` is added,
+ depending on the output file type.
+
+**\---wfiles**
+
+ Use binary w-files in the output whenever possible. The noise-normalization
+ factors can be always output in this format. The current estimates
+ and dSPMs can be output as wfiles if one of the collapse options
+ is selected.
+
+**\---pred <name>**
+
+ Save the predicted data into this file. This is a fif file containing
+ the predicted data waveforms, see Section 6.2.7.
+
+**\---outputnorm <name>**
+
+ Output noise-normalization factors to this file.
+
+**\---invnorm**
+
+ Output inverse noise-normalization factors to the file defined by
+ the ``--outputnorm`` option.
+
+**\---dip <name>**
+
+ Specifies a dipole distribution snapshot file. This is a file containing the
+ current distribution at a time specified with the ``--diptime`` option.
+ The file format is the ASCII dip file format produced by the Neuromag
+ source modelling software (xfit). Therefore, the file can be loaded
+ to the Neuromag MRIlab MRI viewer to display the actual current
+ distribution. This option is only effective if the ``--spm`` option
+ is absent.
+
+**\---diptime <time/ms>**
+
+ Time for the dipole snapshot, see ``--dip`` option above.
+
+**\---label <name>**
+
+ Label to process. The label files are produced by tksurfer 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.
+
+.. note:: The ``--tmin`` and ``--tmax`` options which existed in previous versions of mne_compute_mne have been removed. mne_compute_mne can now process only the entire averaged epoch.
diff --git a/doc/source/manual/AppEULA.rst b/doc/source/manual/AppEULA.rst
new file mode 100644
index 0000000..69eea49
--- /dev/null
+++ b/doc/source/manual/AppEULA.rst
@@ -0,0 +1,133 @@
+
+
+.. _BGBDEIGC:
+
+=================
+Licence agreement
+=================
+
+This appendix includes the terms of the MNE software End-User
+License Agreement (EULA).
+
+License agreement
+#################
+
+THE GENERAL HOSPITAL CORPORATION
+
+ACADEMIC RESEARCH USE
+
+SOFTWARE LICENSE AGREEMENT FOR BINARY CODE
+
+By downloading and/or using the MNE software which is the
+subject of this Agreement (the "Software"), you
+hereby accept and agree to all of the terms and conditions of this
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+
+- *License Grant.* Subject
+ to all of the terms and conditions of this Agreement,\he General
+ Hospital Corporation, d/b/a Massachusetts General Hospital]\he
+ Brigham and Women's Hospital, Inc.] ("Licensor") hereby
+ grants you a non-exclusive, non-transferable, non-sublicensable license
+ under Licensor's rights in the Software to copy and use the binary
+ code of the Software solely for research and educational purposes
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+ Educational Purposes," which term shall include company
+ sponsored research conducted by you in accordance with Institution's
+ policies).
+
+- *No Transfer.* You may not sell, license,
+ distribute, rent, lease, offer on an ASP or service bureau basis,
+ grant a security interest in or otherwise transfer the Software
+ to any third party or use the Software for any commercial purpose.
+
+- *Installation and Maintenance.* You are
+ solely responsible for installing and maintaining the Software and
+ for testing the Software for proper operation. Licensor shall have
+ no obligation to provide any support, maintenance, corrections,
+ debugging, improvements, modifications, upgrades or updates of the
+ Software or notice of any of the forgoing, or otherwise assist Licensee
+ in installing, configuring, integrating, understanding or using
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+
+- *Attributions and Acknowledgments.* You
+ must preserve and maintain all applicable attributions, copyright
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+ You agree to provide acknowledgement of Licensor and its designated
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diff --git a/doc/source/manual/AppInstall.rst b/doc/source/manual/AppInstall.rst
new file mode 100644
index 0000000..2a580e3
--- /dev/null
+++ b/doc/source/manual/AppInstall.rst
@@ -0,0 +1,174 @@
+
+
+.. _BGBDEIGC:
+
+==============================
+Installation and configuration
+==============================
+
+System requirements
+###################
+
+The MNE software runs on Mac OSX and LINUX operating systems.
+The hardware and software requirements are:
+
+- Mac OSX version 10.5 (Leopard) or later.
+
+- LINUX kernel 2.6.9 or later
+
+- On both LINUX and Mac OSX 32-bit and 64-bit Intel platforms
+ are supported. PowerPC version on Mac OSX can be provided upon request.
+
+- At least 2 GB of memory, 4 GB or more recommended.
+
+- Disk space required for the MNE software: 80 MB
+
+- Additional open source software on Mac OSX, see :ref:`BABDBCJE`.
+
+Installation
+############
+
+The MNE software is distributed as a compressed tar archive
+(Mac OSX and LINUX) or a Mac OSX disk image (dmg).
+
+Download the software
+=====================
+
+Download the software package of interest. The file names
+follow the convention:
+
+MNE-*<version>*-<rev> -*<Operating
+system>*-*<Processor>*.*<ext>*
+
+The present version number is 2.7.0. The <rev> field
+is the SVN revision number at the time this package was created.
+The <Operating system> field
+is either Linux or MacOSX. The <processor> field
+is either i386 or x86_64. The <ext> field
+is 'gz' for compressed tar archive files and 'dmg' for
+Mac OSX disk images.
+
+Installing from a compressed tar archive
+========================================
+
+Go to the directory where you want the software to be installed:
+
+``cd`` <dir>
+
+Unpack the tar archive:
+
+``tar zxvf`` <software package>
+
+The name of the software directory under <dir> will
+be the same as the package file without the .gz extension.
+
+Installing from a Mac OSX disk image
+=====================================
+
+- Double click on the disk image file.
+ A window opens with the installer package (<name> .pkg)
+ inside.
+
+- Double click the the package file. The installer starts.
+
+- Follow the instructions in the installer.
+
+.. note:: The software will be installed to /Applications/<name> by default. If you want another location, select Choose Folder... on the Select a Destination screen in the installer.
+
+.. note:: To provide centralized support in an environment with
+
+.. _BABDBCJE:
+
+Additional software
+===================
+
+MNE uses the 'Netpbm' package (http://netpbm.sourceforge.net/)
+to create image files in formats other than tif and rgb from mne_analyze and mne_browse_raw .
+This package is usually present on LINUX systems. On Mac OSX, you
+need to install the netpbm package. The recommended way to do this
+is to use the MacPorts Project tools, see http://www.macports.org/:
+
+- If you have not installed the MacPorts
+ sofware, goto http://www.macports.org/install.php and follow the
+ instructions to install MacPorts.
+
+- Install the netpbm package by saying: ``sudo port install netpbm``
+
+MacPorts requires that you have the XCode developer tools
+and X11 windowing environment installed. X11 is also needed by MNE.
+For Mac OSX Leopard, we recommend using XQuartz (http://xquartz.macosforge.org/).
+As of this writing, XQuartz does not yet exist for SnowLeopard;
+the X11 included with the operating system is sufficient.
+
+.. _CIHIIBDA:
+
+Testing the performance of your OpenGL graphics
+===============================================
+
+The graphics performance of mne_analyze depends
+on your graphics software and hardware configuration. You get the
+best performance if you are using mne_analyze locally
+on a computer and the hardware acceleration capabilities are in
+use. You can check the On GLX... item
+in the help menu of mne_analyze to
+see whether the hardware acceleration is in effect. If the dialog
+popping up says Direct rendering context ,
+you are using hardware acceleration. If this dialog indicates Nondirect rendering context , you are either using software
+emulation locally, rendering to a remote display, or employing VNC
+connection. If you are rendering to a local display and get an indication
+of Nondirect rendering context ,
+software emulation is in effect and you should contact your local
+computer support to enable hardware acceleration for GLX. In some
+cases, this may require acquiring a new graphics display card. Fortunately,
+relatively high-performance OpenGL-capable graphics cards very inexpensive.
+
+There is also an utility mne_opengl_test to
+assess the graphics performance more quantitatively. This utility
+renders an inflated brain surface repeatedly, rotating it by 5 degrees
+around the *z* axis between redraws. At each
+revolution, the time spent for the full revolution is reported on
+the terminal window where mne_opengl_test was
+started from. The program renders the surface until the interrupt
+key (usually control-c) is pressed on the terminal window.
+
+mne_opengl_test is located
+in the ``bin`` directory and is thus started as:
+
+``$MNE_ROOT/bin/mne_opengl_test``
+
+On the fastest graphics cards, the time per revolution is
+well below 1 second. If this time longer than 10 seconds either
+the graphics hardware acceleration is not in effect or you need
+a faster graphics adapter.
+
+Obtain FreeSurfer
+#################
+
+The MNE software relies on the FreeSurfer software for cortical
+surface reconstruction and other MRI-related tasks. Please consult
+the FreeSurfer home page site at ``http://surfer.nmr.mgh.harvard.edu/`` .
+
+How to get started
+##################
+
+After you have installed the software, a good place to start
+is to look at the manual:
+
+- Source the correct setup script, see Section 2.4,
+ and
+
+- Say: ``mne_view_manual`` .
+
+Chapters of interest for a novice user include:
+
+- Chapters 1 and 2 contain introduction
+ to the software and setup instructions.
+
+- Chapter 3 is an overview of the necessary steps to
+ compute the cortically constrained minimum-norm solutions.
+
+- Chapter 12 is a hands-on exercise demonstrating analysis
+ of the sample data set.
+
+- Chapter 13 contains a list of useful references for
+ understanding the methods implemented in the MNE software.
diff --git a/doc/source/manual/AppReleaseNotes.rst b/doc/source/manual/AppReleaseNotes.rst
new file mode 100644
index 0000000..7f3b304
--- /dev/null
+++ b/doc/source/manual/AppReleaseNotes.rst
@@ -0,0 +1,877 @@
+
+
+.. _BGBDEIGC:
+
+=============
+Release notes
+=============
+
+This appendix contains a brief description of the changes
+in MNE software in each major release.
+
+Release notes for MNE software 2.4
+##################################
+
+Manual
+======
+
+The manual has been significantly expanded and reorganized. Chapter 7 describing mne_analyze has
+been added. Chapter 12 contains instructions for analyzing
+the sample data set provided with the software. Useful background
+material is listed in Chapter 13. Almost all utility programs
+are now covered in the manual.
+
+General software changes
+========================
+
+The following overall changes have been made:
+
+- A forward solution library independent
+ of Neuromag software was written.
+
+- The MEG sensor information is now imported from the coil definition file
+ instead of being hardcoded in the software. For details, see Section 5.8.4.
+
+- CTF and 4D Neuroimaging sensors are now supported.
+
+- The number of Neuromag-based utilities was minimized.
+
+- The LINUX port of Neuromag software modules was completely
+ separated from the MNE software and now resides under a separate
+ directory tree.
+
+- Support for topologically connected source spaces was added,
+ see Section 3.5.
+
+- A lot of bugs were fixed.
+
+File conversion utilities
+=========================
+
+The following import utilities were added:
+
+- mne_ctf2fiff to
+ convert CTF data to the fif format, see Section 9.2.2.
+
+- mne_tufts2fiff to convert
+ EEG data from Tufts university to fif format, see Section 9.2.9.
+
+The output of the Matlab conversion utilities was changed
+to use structures. For details, see Sections 9.12, 9.7, and 9.13.
+
+Matlab tools to import and export w and stc files were added.
+
+mne_browse_raw
+==============
+
+Output of decimated and filtered data is now available. mne_analyze now fully
+supports 32-bit integer data found in CTF and new Neuromag raw data
+files.
+
+mne_analyze
+===========
+
+The following changes have been made in mne_analyze :
+
+- Curved and flat surface patches are
+ now supported.
+
+- An iterative coordinate alignment procedure was added, see
+ Section 7.16.
+
+- Utility to view continuous HPI information was added, see Section 7.17.
+
+- Several small changes and bug fixes were done.
+
+mne_make_movie
+==============
+
+The only major change in mne_make_movie is
+the addition of support for curved and surface patches.
+
+Averaging
+=========
+
+The highly inefficient program mne_grand_average has
+been removed from the distribution and replaced with the combined
+use of mne_make_movie and a new
+averaging program mne_average_estimates , see Section 8.6.
+
+Release notes for MNE software 2.5
+##################################
+
+Manual
+======
+
+The MNE Matlab toolbox is now covered in a separate chapter.
+Change bars are employed to indicate changes in the chapters that
+existed in the previous version of the manual. Note that Chapter 10 describing
+the Matlab toolbox is totally new and change bars have not been
+used there. Furthermore, Appendix B now contains all the
+information specific to the Martinos Center.
+
+mne_browse_raw
+==============
+
+There are several improvements in the raw data processor mne_browse_raw/mne_process_raw :
+
+- Possibility to delete and add channel
+ selections interactively has been added. A nonstandard channel selection
+ file can be now specified on the command line.
+
+- Handling of CTF software gradient compensation has been added.
+
+- The vertical scale of the digital trigger channel is now automatically
+ set to accommodate the largest trigger value.
+
+- It is now possible to load evoked-response data sets from
+ files. Time scales of the evoked-response data and data averaged
+ in mne_browse_raw can be now
+ set from the scales dialog. Section 12.9 in Chapter 12 has
+ been updated to employ mne_browse_raw in
+ viewing the averages computed from the sample raw data set.
+
+- It is now possible to create new SSP operators in mne_browse_raw ,
+ see Section 4.6.4.
+
+- Listing of amplitude values have been added to both the strip-chart
+ and topographical displays.
+
+- Text format event files can now be loaded for easy inspection
+ of rejected epochs, for example.
+
+- Handling of derived channels has been added, see Sections 4.4.12 and 11.5.
+
+- SSS information is now transferred to the covariance matrix
+ output files.
+
+- Neuromag processing history is included with the output files.
+
+mne_epochs2mat
+==============
+
+This new utility extracts epochs from a raw data file, applies
+a bandpass filter to them and outputs them in a format convenient
+for processing in Matlab, see Section 9.14.
+
+mne_analyze
+===========
+
+The following new features have been added:
+
+- Processing of raw data segment and easy
+ switching between multiple evoked data sets (not in the manual yet).
+
+- Sketchy surface display mode for source spaces with selection
+ triangulation information created with the ``--ico`` option
+ to mne_setup_source_space .
+
+- Rotation of the coordinate frame in the coordinate system
+ alignment dialog, see Section 7.16;
+
+- Several new graphics output file formats as well as automatic
+ and snapshot output modes, see Section 7.8.8.
+
+- It is now possible to inquire timecourses from stc overlays.
+ Both labels and surface picking are supported.
+
+- Added an option to include surface vertex numbers to the timecourse output,
+ see Section 7.13.3.1.
+
+- Overlays matching the scalp surface can now be loaded, see Section 7.14.
+
+- The dipole display dialog has now control over the dipole
+ display properties. Multiple dipoles can be now displayed, see Section 7.15.3.
+
+- Time stepping with cursor keys has been added.
+
+- Dynamic cursors have been added to the full view display.
+
+- The viewer display now automatically rotates to facilitate
+ fiducial picking from the head surface.
+
+mne_ctf2fiff
+============
+
+Correct errors in compensation channel information and compensation data
+output. The transformation between the CTF and Neuromag coordinate
+frames is now included in the output file.
+
+mne_make_movie
+==============
+
+Added the ``--labelverts`` option, see Section 6.5.8.
+
+mne_surf2bem
+============
+
+Added the ``--shift`` option to move surface vertices
+outwards. Fixed some loopholes in topology checks. Also added the ``--innershift`` option
+to mne_setup_forward_model . For
+more information, see Sections 3.7 and 5.6.
+
+mne_forward_solution
+====================
+
+Added code to compute forward solutions for CTF data with
+software gradient compensation on.
+
+mne_inverse_operator
+====================
+
+The following changes have been made in mne_inverse_operator :
+
+- Added options to regularize the noise-covariance
+ matrix.
+
+- Added correct handling of the rank-deficient covariance matrix
+ resulting from the use of SSS.
+
+- Additional projections cannot be specified if the noise covariance matrix
+ was computed with projections on.
+
+- Bad channels can be added only in special circumstances if
+ the noise covariance matrix was computed with projections on.
+
+mne_compute_raw_inverse
+=======================
+
+This utility is now documented in Section 6.6. The
+utility mne_make_raw_inverse_operator has
+been removed from the software.
+
+Time range settings
+===================
+
+The tools mne_compute_raw_inverse , mne_convert_mne_data ,
+and mne_compute_mne no longer
+have command-line options to restrict the time range of evoked data
+input.
+
+mne_change_baselines
+====================
+
+It is now possible to process all data sets in a file at
+once. All processed data are stored in a single output file.
+
+New utilities
+=============
+
+mne_show_fiff
+-------------
+
+Replacement for the Neuromag utility show_fiff .
+This utility conforms to the standard command-line option conventions
+in MNE software. For details, see Section 11.3.
+
+mne_make_cor_set
+----------------
+
+Replaces the functionality of the Neuromag utility create_mri_set_simple to
+create a fif format description file for the FreeSurfer MRI data.
+This utility is called by the mne_setup_mri script.
+
+mne_compensate_data
+-------------------
+
+This utility applies or removes CTF software gradient compensation
+from evoked-response data, see Section 9.2.4.
+
+mne_insert_4D_comp
+------------------
+
+This utility merges 4D Magnes compensation data from a text
+file and the main helmet sensor data from a fif file and creates
+a new fif file Section 9.2.5.
+
+mne_ctf_dig2fiff
+----------------
+
+This utility reads a text format Polhemus data file, transforms
+the data into the Neuromag head coordinate system, and outputs the
+data in fif or hpts format.
+
+mne_kit2fiff
+------------
+
+The purpose of this new utility is to import data from the
+KIT MEG system, see Section 9.2.7.
+
+mne_make_derivations
+--------------------
+
+This new utility will take derivation data from a text file
+and convert it to fif format for use with mne_browse_raw ,
+see Section 11.5.
+
+BEM mesh generation
+===================
+
+All information concerning BEM mesh generation has been moved
+to Appendix A. Utilities for BEM mesh generation using
+FLASH images have been added, see Section A.2.
+
+Matlab toolbox
+==============
+
+The MNE Matlab toolbox has been significantly enhanced. New
+features include:
+
+- Basic routines for reading and writing
+ fif files.
+
+- High-level functions to read and write evoked-response fif
+ data.
+
+- High-level functions to read raw data.
+
+- High-level routines to read source space information, covariance
+ matrices, forward solutions, and inverse operator decompositions
+ directly from fif files.
+
+The Matlab toolbox is documented in Chapter 10.
+
+The mne_div_w utility
+has been removed because it is now easy to perform its function
+and much more using the Matlab Toolbox.
+
+Release notes for MNE software 2.6
+##################################
+
+Manual
+======
+
+The changes described below briefly are documented in the
+relevant sections of the manual. Change bars are employed to indicate
+changes with respect to manual version 2.5. Chapter 5 now
+contains a comprehensive discussion of the various coordinate systems
+used in MEG/EEG data.
+
+Command-line options
+====================
+
+All compiled C programs now check that the command line does
+not contain any unknown options. Consequently, scripts that have
+inadvertently specified some options which are invalid will now
+fail.
+
+Changes to existing software
+============================
+
+mne_add_patch_info
+------------------
+
+- Changed option ``--in`` to ``--src`` and ``--out`` to ``--srcp`` .
+
+- Added ``--labeldir`` option.
+
+mne_analyze
+-----------
+
+New features include:
+
+- The name of the digital trigger channel
+ can be specified with the MNE_TRIGGER_CH_NAME environment variable.
+
+- Using information from the fif data files, the wall clock
+ time corresponding to the current file position is shown on the
+ status line
+
+- mne_analyze can now be
+ controlled by mne_browse_raw to
+ facilitate interactive analysis of clinical data.
+
+- Added compatibility with Elekta-Neuromag Report Composer (cliplab and
+ improved the quality of hardcopies.
+
+- Both in mne_browse_raw and
+ in mne_analyze , a non-standard
+ default layout can be set on a user-by-user basis, see Section 4.5.6.
+
+- Added the ``--digtrigmask`` option.
+
+- Added new image rotation functionality using the mouse wheel
+ or trackball.
+
+- Added remote control of the FreeSurfer MRI
+ viewer (tkmedit ), see Section 7.18.
+
+- Added fitting of single equivalent current dipoles and channel
+ selections, see Section 7.15.
+
+- Added loading of FreeSurfer cortical
+ parcellation data as labels.
+
+- Added support for using the FreeSurfer average
+ brain (fsaverage) as a surrogate.
+
+- The surface selection dialog was redesigned for faster access
+ to the files and to remove problems with a large number of subjects.
+
+- A shortcut button to direct a file selector to the appropriate
+ default directory was added to several file loading dialogs.
+
+- The vertex coordinates can now be displayed, see Section 7.8.4.
+
+mne_average_forward_solutions
+-----------------------------
+
+EEG forward solutions are now averaged as well, see Section 5.10.
+
+mne_browse_raw and mne_process_raw
+----------------------------------
+
+Improvements in the raw data processor mne_browse_raw /mne_process_raw include:
+
+- The name of the digital trigger channel
+ can be specified with the MNE_TRIGGER_CH_NAME environment variable.
+
+- The format of the text event files was slightly changed. The
+ sample numbers are now "absolute" sample numbers
+ taking into account the initial skip in the event files. The new
+ format is indicated by an additional "pseudoevent" in
+ the beginning of the file. mne_browse_raw and mne_process_raw are
+ still compatible with the old event file format. For details, see Section 4.10.5.
+
+- Using information from the fif data files, the wall clock
+ time corresponding to the current file position is shown on the
+ status line
+
+- mne_browse_raw can now
+ control mne_analyze to facilitate
+ interactive analysis of clinical data.
+
+- If the length of an output raw data file exceeds the 2-Gbyte
+ fif file size limit, the output is split into multiple files.
+
+- ``-split`` and ``--events`` options was
+ added to mne_process_raw .
+
+- The ``--allowmaxshield`` option was added to mne_browse_raw to allow
+ loading of unprocessed data with MaxShield in the Elekta-Neuromag
+ systems. These kind of data should never be used as an input for source
+ localization.
+
+- The ``--savehere`` option was added, see Section 4.2.3.
+
+- The stderr parameter was
+ added to the averaging definition files, see Section 4.13.3.
+
+- Added compatibility with Elekta-Neuromag Report Composer (cliplab and
+ improved the quality of hardcopies.
+
+- Both in mne_browse_raw and
+ in mne_analyze , a non-standard
+ default layout can be set on a user-by-user basis, see Section 4.5.6.
+
+- mne_browse_raw now includes
+ an interactive editor to create derived channels, see Section 4.5.4.
+
+- The menus in mne_browse_raw were
+ reorganized and an time point specification text field was added
+
+- Possibility to keep the old projection items added to the
+ new projection definition dialog.
+
+- Added ``--cd`` option.
+
+- Added filter buttons for raw files and Maxfilter (TM) output
+ to the open dialog.
+
+- Added possibility to create a graph-compatible projection
+ to the Save projection dialog
+
+- Added possibility to compute a projection operator from epochs
+ specified by events.
+
+- Added the keepsamplemean option
+ to the covariance matrix computation files.
+
+- Added the ``--digtrigmask`` option.
+
+- Added Load channel selections... item
+ to the File menu.
+
+- Added new browsing functionality using the mouse wheel or
+ trackball, see Section 4.9.1.
+
+- Added optional items to the topographical data displays, see Section 4.5.2.
+
+- Added an event list window, see Section 4.10.2.
+
+- Added an annotator window, see Section 4.10.4.
+
+- Keep events sorted by time.
+
+- User-defined events are automatically kept in a fif-format
+ annotation file, see Section 4.10.
+
+- Added the delay parameter
+ to the averaging and covariance matrix estimation description files,
+ see Sections 4.13.3 and 4.14.3.
+
+Detailed information on these changes can be found in Chapter 4.
+
+mne_compute_raw_inverse
+-----------------------
+
+The ``--digtrig`` , ``--extra`` , ``--noextra`` , ``--split`` , ``--labeldir`` , and ``--out`` options
+were added, see Section 6.6.
+
+mne_convert_surface
+-------------------
+
+The functionality of mne_convert_dfs was
+integrated into mne_convert_surface .
+Text output as a triangle file and and file file containing the
+list of vertex points was added. The Matlab output option was removed.
+Consequently, mne_convert_dfs , mne_surface2mat ,
+and mne_list_surface_nodes were
+deleted from the distribution.
+
+mne_dump_triggers
+-----------------
+
+This obsolete utility was deleted from the distribution.
+
+mne_epochs2mat
+--------------
+
+The name of the digital trigger channel can be specified
+with the MNE_TRIGGER_CH_NAME environment variable, see Section 9.14. Added
+the ``--digtrigmask`` option.
+
+mne_forward_solution
+--------------------
+
+Added code to compute the derivatives of with respect to
+the dipole position coordinates, see Section 5.9.
+
+mne_list_bem
+------------
+
+The --surfno option is replaced with the --id option, see Section 9.6.
+
+mne_make_cor_set
+----------------
+
+Include data from mgh/mgz files to the output automatically.
+Include the Talairach transformations from the FreeSurfer data to
+the output file if possible. For details, see Section 9.8.
+
+mne_make_movie
+--------------
+
+Added the --noscalebar, --nocomments, --morphgrade, --rate,
+and --pickrange options, see Section 6.5.
+
+mne_make_source_space
+---------------------
+
+The ``--spacing`` option is now implemented in this
+program, which means mne_mris_trix is
+now obsolete. The mne_setup_source_space script
+was modified accordingly. Support for tri, dec, and dip files was dropped,
+see Section 5.4.
+
+mne_mdip2stc
+------------
+
+This utility is obsolete and was removed from the distribution.
+
+mne_project_raw
+---------------
+
+This is utility is obsolete and was removed from the distribution.
+The functionality is included in mne_process_raw .
+
+mne_rename_channels
+-------------------
+
+Added the ``--revert`` option, see Section 11.4.5.
+
+mne_setup_forward_model
+-----------------------
+
+Added the ``--outershift`` and ``--scalpshift`` options,
+see Section 3.7.
+
+mne_simu
+--------
+
+Added source waveform expressions and the ``--raw`` option,
+see Section 11.13.
+
+mne_transform_points
+--------------------
+
+Removed the ``--tomrivol`` option.
+
+Matlab toolbox
+--------------
+
+Several new functions were added, see Chapter 10.
+
+.. note:: The matlab function fiff_setup_read_raw has a significant change. The sample numbers now take into account possible intial 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 indentically with the previous version, subt [...]
+
+New utilities
+=============
+
+mne_collect_transforms
+----------------------
+
+This utility collects coordinate transformation information
+from several sources into a single file, see Section 9.9.
+
+mne_convert_dig_data
+--------------------
+
+This new utility convertes digitization (Polhemus) data between
+different file formats, see Section 9.3.
+
+mne_edf2fiff
+------------
+
+This is a new utility to convert EEG data from EDF, EDF+,
+and BDF formats to the fif format, see Section 9.2.8.
+
+mne_brain_vision2fiff
+---------------------
+
+This is a new utility to convert BrainVision EEG data to
+the fif format, see Section 9.2.10. This utility is also
+used by the mne_eximia_2fiff script
+to convert EEG data from the Nexstim eXimia EEG system to the fif
+format, see Section 9.2.11.
+
+mne_anonymize
+-------------
+
+New utility to remove subject identifying information from
+measurement files, see Section 11.4.7.
+
+mne_opengl_test
+---------------
+
+New utility for testing the OpenGL graphics performance,
+see Section C.2.5.
+
+mne_volume_data2mri
+-------------------
+
+Convert data defined in a volume created with mne_volume_source_space to
+an MRI overlay, see Section 9.4.
+
+mne_volume_source_space
+-----------------------
+
+Create a a grid of source points within a volume, see Section 5.5. mne_volume_source_space also
+optionally creates a trilinear interpolator matrix to facilitate
+converting values a distribution in the volume grid into an MRI
+overlay using mne_volume_data2mri ,
+see Section 9.4.
+
+mne_copy_processing_history
+---------------------------
+
+This new utility copies the processing history block from
+one data file to another, see Section 11.4.8.
+
+Release notes for MNE software 2.7
+##################################
+
+Software engineering
+====================
+
+There have been two significant changes in the software engineering
+since MNE Version 2.6:
+
+- CMake is now used in building the software
+ package and
+
+- Subversion (SVN) is now used for revision control instead
+ of Concurrent Versions System (CVS).
+
+These changes have the effects on the distribution of the
+MNE software and setup for individual users:
+
+- There is now a separate software package
+ for each of the platforms supported.
+
+- The software is now organized completely under standard directories (bin,
+ lib, and share). In particular, the directory setup/mne has been moved
+ to share/mne and the directories app-defaults and doc are now under
+ share. All files under share are platform independent.
+
+- The use of shared libraries has been minimized. This alleviates
+ compatibility problems across operating system versions.
+
+- The setup scripts have changed.
+
+The installation and user-level effects of the new software
+organization are discussed in Chapter 2 and Appendix C.
+
+In addition, several minor bugs have been fixed in the source
+code. Most relevant changes visible to the user are listed below.
+
+Matlab tools
+============
+
+- The performance of the fiff I/O routines
+ has been significantly improved thanks to the contributions of François
+ Tadel at USC.
+
+- Label file I/O routines mne_read_label_file and mne_write_label_file as
+ well as a routine to extract time courses corresponding to a label from
+ an stc file (mne_label_time_courses) have been added.
+
+- The patch information is now read from the source space file
+ and included in the source space data structure.
+
+mne_browse_raw
+==============
+
+- Rejection criteria to detect flat channels
+ have been added, see Sections 4.13.2 and 4.14.2.
+
+- Possibility to detect temporal skew between trigger input
+ lines has been added, see Sections 4.13.2 and 4.14.2.
+
+- --allowmaxshield option now works in the batch mode as well.
+
+- Added the --projevent option to batch mode.
+
+- It is now possible to compute an SSP operator for EEG, see Section 4.6.4.
+
+mne_analyze
+===========
+
+- Both hemispheres can now be displayed
+ simultaneously, see Section 7.8.3.
+
+- If the source space was created with mne_make_source_space version 2.3
+ or later, the subject's surface data are automatically
+ loaded after loading the data and the inverse operator.
+
+Miscellaneous
+=============
+
+- mne_smooth_w was
+ renamed to mne_smooth and can
+ now handle both w and stc files. Say ``mne_smooth --help`` to
+ find the options.
+
+- All binaries now reside in $MNE_ROOT/bin. There are no separate bin/mne
+ and bin/admin directories.
+
+- mne_anonymize now has the
+ --his option to remove the HIS ID of the subject, see Section 11.4.7,
+
+- mne_check_surface now has
+ the --bem and --id options to check surfaces from a BEM fif file.
+ For details, try mne_check_surface --help.
+
+- mne_compute_raw_inverse now
+ has the --orignames option, see Section 6.6.1.
+
+- Added --headcoord option to mne_convert_dig_data ,
+ see Section 9.3.
+
+- Added --talairach option to mne_make_cor_set ,
+ see Section 9.8.
+
+- Added the --morph option to mne_setup_source_space and mne_make_source_space ,
+ see Sections 3.5 and 5.4, respectively.
+
+- Added the --prefix option to mne_morph_labels ,
+ see Section 8.5.
+
+- Added the --blocks and --indent options to mne_show_fiff ,
+ see Section 11.3.
+
+- Added the --proj option as well as map types 5 and 6 to mne_sensitivity_map ,
+ see Section 11.10.
+
+- Fixed a bug in mne_inverse_operator which
+ caused erroneous calculation of EEG-only source estimates if the
+ data were processed with Maxfilter software and sometimes caused
+ similar behavior on MEG/EEG source estimates.
+
+Release notes for MNE software 2.7.1
+####################################
+
+mne_analyze
+===========
+
+- Added a new restricted mode for visualizing
+ head position within the helmet, see Sections 7.2 and 7.21.
+
+- Added information about mne_make_scalp_surfaces to Section 7.16.1.
+
+mne_browse_raw
+==============
+
+- Added possibility for multiple event
+ parameters and the mask parameter in averaging and noise covariance
+ calculation, see Section 4.13.3.
+
+- Added simple conditional averaging, see Section 4.13.3.
+
+Release notes for MNE software 2.7.2
+####################################
+
+mne_add_patch_info
+==================
+
+Added the capability to compute distances between source
+space vertices, see Section 11.7.
+
+Matlab toolbox
+==============
+
+- Added new functions to for stc and w
+ file I/O to employ 1-based vertex numbering inside Matlab, see Table 10.11.
+
+- mne_read_source_spaces.m now reads the inter-vertex distance
+ information now optionally produced by mne_add_patch_info ,
+ see Section 11.7.
+
+Miscellaneous
+=============
+
+- Added --shift option to mne_convert_surface ,
+ see Section 9.7.1.
+
+- Added --alpha option to mne_make_movie ,
+ see Section 6.5.5.
+
+- Added --noiserank option to mne_inverse_operator and mne_do_inverse_operator ,
+ see Sections 6.4 and 3.13, respectively.
+
+- The fif output from mne_convert_dig_data now
+ includes the transformation between the digitizer and MNE head coordinate
+ systems if such a transformation has been requested, see Section 9.3.
+ This also affects the output from mne_eximia2fiff, see Section 9.2.11.
+
+- Added --noflash30, --noconvert, and --unwarp options to mne_flash_bem ,
+ see Section A.2.
+
+Release notes for MNE software 2.7.3
+####################################
+
+Miscellaneous
+=============
+
+- Added preservation of the volume geometry
+ information in the FreeSurfer surface files.
+
+- The --mghmri option in combination with --surfout inserts
+ the volume geometry information to the output of mne_convert_surface ,
+ see Section 9.7.
+
+- Added --replacegeom option to mne_convert_surface ,
+ see Section 9.7.
+
+- Modified mne_watershed_bem and mne_flash_bem to
+ include the volume geometry information to the output. This allows
+ viewing of the output surfaces in the FreeSurfer freeview utility.
diff --git a/doc/source/manual/utilities.rst b/doc/source/manual/utilities.rst
index b063fff..afbdced 100644
--- a/doc/source/manual/utilities.rst
+++ b/doc/source/manual/utilities.rst
@@ -611,7 +611,7 @@ The command-line options are:
.. _BEHCBCGG:
Adding neighborhood/topology information to source spaces
-################################################
+#########################################################
Purpose
=======
--
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