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. Interactive analysis with mne_analyze describing mne_analyze has been added. The sample data set contains instructions for analyzing the sample data set provided with the software. Useful background material is listed in Related publications. 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.
  • 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.
  • 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.
  • mne_tufts2fiff to convert EEG data from Tufts university to fif format.

The output of the Matlab conversion utilities was changed to use structures.

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 Coordinate frame alignment.
  • Utility to view continuous HPI information was added.
  • 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.

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 MNE-MATLAB toolbox describing the Matlab toolbox is totally new and change bars have not been used there. Furthermore, Setup at the Martinos Center 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. Viewing the off-line average 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.
  • 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.
  • 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.

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.
  • Several new graphics output file formats as well as automatic and snapshot output modes.
  • 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.
  • Overlays matching the scalp surface can now be loaded.
  • The dipole display dialog has now control over the dipole display properties. Multiple dipoles can be now displayed.
  • 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.

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.

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 Computing inverse from raw and evoked data. 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.

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.

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 mne_insert_4D_comp.

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.

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.

BEM mesh generation

All information concerning BEM mesh generation has been moved to Creating the BEM meshes. Utilities for BEM mesh generation using FLASH images have been added.

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 MNE-MATLAB toolbox.

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. The forward solution 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.
  • Added the --digtrigmask option.
  • Added new image rotation functionality using the mouse wheel or trackball.
  • Added remote control of the FreeSurfer MRI viewer (tkmedit ).
  • Added fitting of single equivalent current dipoles and channel selections.
  • 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.

mne_average_forward_solutions

EEG forward solutions are now averaged as well.

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.
  • 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.
  • The stderr parameter was added to the averaging definition files.
  • 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.
  • mne_browse_raw now includes an interactive editor to create derived channels.
  • 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.
  • Added optional items to the topographical data displays.
  • Added an event list window.
  • Added an annotator window.
  • Keep events sorted by time.
  • User-defined events are automatically kept in a fif-format annotation file.
  • Added the delay parameter to the averaging and covariance matrix estimation description files.

Detailed information on these changes can be found in Browsing raw data with mne_browse_raw.

mne_compute_raw_inverse

The --digtrig , --extra , --noextra , --split , --labeldir , and --out options were added.

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. Added the --digtrigmask option.

mne_forward_solution

Added code to compute the derivatives of with respect to the dipole position coordinates.

mne_list_bem

The --surfno option is replaced with the --id option.

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.

mne_make_movie

Added the --noscalebar, --nocomments, --morphgrade, --rate, and --pickrange options.

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.

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.

mne_setup_forward_model

Added the --outershift and --scalpshift options.

mne_simu

Added source waveform expressions and the --raw option.

mne_transform_points

Removed the --tomrivol option.

Matlab toolbox

Several new functions were added, see MNE-MATLAB toolbox.

Note

The matlab function fiff_setup_read_raw has a significant change. The sample numbers now take into account possible initial skip in the file, i.e., the time between the start of the data acquisition and the start of saving the data to disk. The first_samp member of the returned structure indicates the initial skip in samples. If you want your own routines, which assume that initial skip has been removed, perform indentically with the previous version, subtract first_samp from the sample numbers you specify to fiff_read_raw_segment . Furthermore, fiff_setup_read_raw has an optional argument to allow reading of unprocessed MaxShield data acquired with the Elekta MEG systems.

New utilities

mne_collect_transforms

This utility collects coordinate transformation information from several sources into a single file.

mne_convert_dig_data

This new utility convertes digitization (Polhemus) data between different file formats.

mne_edf2fiff

This is a new utility to convert EEG data from EDF, EDF+, and BDF formats to the fif format.

mne_brain_vision2fiff

This is a new utility to convert BrainVision EEG data to the fif format. 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.

mne_anonymize

New utility to remove subject identifying information from measurement files.

mne_opengl_test

New utility for testing the OpenGL graphics performance.

mne_volume_data2mri

Convert data defined in a volume created with mne_volume_source_space to an MRI overlay.

mne_volume_source_space

Create a a grid of source points within a volume. 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.

mne_copy_processing_history

This new utility copies the processing history block from one data file to another.

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 Install MNE-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.
  • Possibility to detect temporal skew between trigger input lines has been added.
  • --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.

mne_analyze

  • Both hemispheres can now be displayed simultaneously.
  • 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.
  • mne_check_surface now has the --bem and --id options to check surfaces from a BEM fif file.
  • mne_compute_raw_inverse now has the --orignames option.
  • Added --headcoord option to mne_convert_dig_data.
  • Added --talairach option to mne_make_cor_set.
  • Added the --morph option to mne_setup_source_space and mne_make_source_space.
  • Added the --prefix option to mne_morph_labels.
  • Added the --blocks and --indent options to mne_show_fiff.
  • Added the --proj option as well as map types 5 and 6 to mne_sensitivity_map.
  • 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

mne_browse_raw

  • Added possibility for multiple event parameters and the mask parameter in averaging and noise covariance calculation.
  • Added simple conditional averaging.

Release notes for MNE software 2.7.2

mne_add_patch_info

Added the capability to compute distances between source space vertices.

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.

Miscellaneous

  • Added --shift option to mne_convert_surface.
  • Added --alpha option to mne_make_movie.
  • Added --noiserank option to mne_inverse_operator and mne_do_inverse_operator.
  • 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. This also affects the output from mne_eximia2fiff.
  • Added --noflash30, --noconvert, and --unwarp options to mne_flash_bem.

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.
  • Added --replacegeom option to mne_convert_surface.
  • 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.