This appendix contains a brief description of the changes in MNE software in each major release.
The manual has been significantly expanded and reorganized. Interactive analysis 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.
The following overall changes have been made:
The following import utilities were added:
The output of the Matlab conversion utilities was changed to use structures. For details, see The MNE data file conversion tool, Converting surface data between different formats, and Converting raw data to Matlab format.
Matlab tools to import and export w and stc files were added.
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.
The following changes have been made in mne_analyze :
The only major change in mne_make_movie is the addition of support for curved and surface patches.
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 The 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.
There are several improvements in the raw data processor mne_browse_raw/mne_process_raw :
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 Converting epochs to Matlab format.
The following new features have been added:
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.
Added the --labelverts option, see Label processing.
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 Setting up the boundary-element model and Creating the BEM meshes.
Added code to compute forward solutions for CTF data with software gradient compensation on.
The following changes have been made in mne_inverse_operator :
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.
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.
It is now possible to process all data sets in a file at once. All processed data are stored in a single output file.
Replacement for the Neuromag utility show_fiff . This utility conforms to the standard command-line option conventions in MNE software. For details, see Listing contents of a fif file.
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.
This utility applies or removes CTF software gradient compensation from evoked-response data, see Applying software gradient compensation.
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 Importing Magnes compensation channel data.
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.
The purpose of this new utility is to import data from the KIT MEG system, see Importing KIT MEG system data.
This new utility will take derivation data from a text file and convert it to fif format for use with mne_browse_raw , see Creating a derivation file.
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, see Using FLASH images.
The MNE Matlab toolbox has been significantly enhanced. New features include:
The Matlab toolbox is documented in The 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.
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.
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.
New features include:
EEG forward solutions are now averaged as well, see Averaging forward solutions.
Improvements in the raw data processor mne_browse_raw /mne_process_raw include:
Detailed information on these changes can be found in Processing raw data.
The --digtrig , --extra , --noextra , --split , --labeldir , and --out options were added, see Computing inverse from raw and evoked data.
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.
This obsolete utility was deleted from the distribution.
The name of the digital trigger channel can be specified with the MNE_TRIGGER_CH_NAME environment variable, see Converting epochs to Matlab format. Added the --digtrigmask option.
Added code to compute the derivatives of with respect to the dipole position coordinates, see Computing the forward solution.
The --surfno option is replaced with the --id option, see Listing BEM mesh data.
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 Converting MRI data into the fif format.
Added the --noscalebar, --nocomments, --morphgrade, --rate, and --pickrange options, see Producing movies and snapshots.
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 Creating a surface-based source space.
This utility is obsolete and was removed from the distribution.
This is utility is obsolete and was removed from the distribution. The functionality is included in mne_process_raw .
Added the --revert option, see Modifying channel names and types: mne_rename_channels.
Added the --outershift and --scalpshift options, see Setting up the boundary-element model.
Added source waveform expressions and the --raw option, see Data simulator.
Removed the --tomrivol option.
Several new functions were added, see The Matlab toolbox.
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, 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.
This utility collects coordinate transformation information from several sources into a single file, see Collecting coordinate transformations into one file.
This new utility convertes digitization (Polhemus) data between different file formats, see Converting digitization data.
This is a new utility to convert EEG data from EDF, EDF+, and BDF formats to the fif format, see Importing EEG data saved in the EDF, EDF+, or BDF format.
This is a new utility to convert BrainVision EEG data to the fif format, see Importing BrainVision EEG data. 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 Converting eXimia EEG data.
New utility to remove subject identifying information from measurement files, see Removing identifying information.
New utility for testing the OpenGL graphics performance, see Testing the performance of your OpenGL graphics.
Convert data defined in a volume created with mne_volume_source_space to an MRI overlay, see Converting volumetric data into an MRI overlay.
Create a a grid of source points within a volume, see Creating a volumetric or discrete source space. 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 Converting volumetric data into an MRI overlay.
This new utility copies the processing history block from one data file to another, see Copying the processing history.
There have been two significant changes in the software engineering since MNE Version 2.6:
These changes have the effects on the distribution of the MNE software and setup for individual users:
The installation and user-level effects of the new software organization are discussed in Overview and Setup at the Martinos Center.
In addition, several minor bugs have been fixed in the source code. Most relevant changes visible to the user are listed below.
Added the capability to compute distances between source space vertices, see Adding neighborhood/topology information to source spaces.