The principal components of the MNE Software and their functions are listed in The software components.. Documented software is listed in italics. Utility programs. lists various supplementary utilities.
| Name | Purpose |
|---|---|
| mne_analyze | An interactive analysis tool for computing source estimates, see Interactive analysis. |
| mne_average_estimates | Average data across subjects, see The averager. |
| mne_browse_raw | Interactive raw data browser. Includes filtering, offline averaging, and computation of covariance matrices, see Processing raw data. |
| mne_compute_mne | Computes the minimum-norm estimates, see mne_compute_mne. Most of the functionality of mne_compute_mne is included in mne_make_movie. |
| mne_compute_raw_inverse | Compute the inverse solution from raw data see Computing inverse from raw and evoked data. |
| mne_convert_mne_data | Convert MNE data files to other file formats, see The MNE data file conversion tool. |
| mne_do_forward_solution | Convenience script to calculate the forward solution matrix, see Computing the forward solution. |
| mne_do_inverse_operator | Convenience script for inverse operator decomposition, see Calculating the inverse operator decomposition. |
| mne_forward_solution | Calculate the forward solution matrix, see Computing the forward solution. |
| mne_inverse_operator | Compute the inverse operator decomposition see Inverse-operator decomposition. |
| mne_make_movie | Make movies in batch mode, see Producing movies and snapshots. |
| mne_make_source_space | Create a fif source space description file, see Creating a surface-based source space. |
| mne_process_raw | A batch-mode version of mne_browse_raw, see Processing raw data. |
| mne_redo_file | Many intermediate result files contain a description of their ‘production environment’. Such files can be recreated easily with this utility. This is convenient if, for example, the selection of bad channels is changed and the inverse operator decomposition has to be recalculated. |
| mne_redo_file_nocwd | Works like mne_redo_file but does not try to change in to the working directory specified in the ‘production environment’. |
| mne_setup_forward_model | Set up the BEM-related fif files, see Setting up the boundary-element model. |
| mne_setup_mri | A convenience script to create the fif files describing the anatomical MRI data, see Setting up the anatomical MR images for MRIlab |
| mne_setup_source_space | A convenience script to create source space description file, see Setting up the source space. |
| mne_show_environment | Show information about the production environment of a file. |
| Name | Purpose |
|---|---|
| mne_add_patch_info | Add neighborhood information to a source space file, see Adding neighborhood/topology information to source spaces. |
| mne_add_to_meas_info | Utility to add new information to the measurement info block of a fif file. The source of information is another fif file. |
| mne_add_triggers | Modify the trigger channel STI 014 in a raw data file, see Modifying trigger channel data: mne_add_triggers. The same effect can be reached by using an event file for averaging in mne_process_raw and mne_browse_raw. |
| mne_annot2labels | Convert parcellation data into label files, see Converting parcellation data into labels. |
| mne_anonymize | Remove subject-specific information from a fif data file, see Removing identifying information. |
| mne_average_forward_solutions | Calculate an average of forward solutions, see Averaging forward solutions. |
| mne_brain_vision2fiff | Convert EEG data from BrainVision format to fif format, see Importing BrainVision EEG data. |
| mne_change_baselines | Change the dc offsets according to specifications given in a text file, see Inquiring and changing baselines. |
| mne_change_nave | Change the number of averages in an evoked-response data file. This is often necessary if the file was derived from several files. |
| mne_check_eeg_locations | Checks that the EEG electrode locations have been correctly transferred from the Polhemus data block to the channel information tags, see Updating EEG location info: mne_check_eeg_locations. |
| mne_check_surface | Check the validity of a FreeSurfer surface file or one of the surfaces within a BEM file. This program simply checks for topological errors in surface files. |
| mne_collect_transforms | Collect coordinate transformations from several sources into a single fif file, see Collecting coordinate transformations into one file. |
| mne_compensate_data | Change the applied software gradient compensation in an evoked-response data file, see Applying software gradient compensation. |
| mne_convert_lspcov | Convert the LISP format noise covariance matrix output by graph into fif, see Converting a lisp covariance matrix to fiff. |
| mne_convert_ncov | Convert the ncov format noise covariance file to fif, see Converting an ncov covariance matrix file to fiff. |
| mne_convert_surface | Convert FreeSurfer and text format surface files into Matlab mat files, see Converting surface data between different formats. |
| mne_cov2proj | Pick eigenvectors from a covariance matrix and create a signal-space projection (SSP) file out of them, see Fitting a sphere to a surface. |
| mne_create_comp_data | Create a fif file containing software gradient compensation information from a text file, see Creating software gradient compensation data. |
| mne_ctf2fiff | Convert a CTF ds folder into a fif file, see Importing CTF data. |
| mne_ctf_dig2fiff | Convert text format digitization data to fif format, see Importing CTF Polhemus data. |
| mne_dicom_essentials | List essential information from a DICOM file. This utility is used by the script mne_organize_dicom, see Organizing MRI data into directories. |
| mne_edf2fiff | Convert EEG data from the EDF/EDF+/BDF formats to the fif format, see Importing data from other MEG/EEG systems. |
| mne_epochs2mat | Apply bandpass filter to raw data and extract epochs for subsequent processing in Matlab, see Converting epochs to Matlab format. |
| mne_evoked_data_summary | List summary of averaged data from a fif file to the standard output. |
| mne_eximia2fiff | Convert EEG data from the Nexstim eXimia system to fif format, see Converting eXimia EEG data. |
| mne_fit_sphere_to_surf | Fit a sphere to a surface given in fif or FreeSurfer format, see Fitting a sphere to a surface. |
| mne_fix_mag_coil_types | Update the coil types for magnetometers in a fif file, see Updating magnetometer coil types: mne_fix_mag_coil_types. |
| mne_fix_stim14 | Fix coding errors of trigger channel STI 014, see Cleaning the digital trigger channel. |
| mne_flash_bem | Create BEM tessellation using multi-echo FLASH MRI data, see Using FLASH images. |
| mne_insert_4D_comp | Read Magnes compensation channel data from a text file and merge it with raw data from other channels in a fif file, see Importing Magnes compensation channel data. |
| mne_list_bem | List BEM information in text format, see Listing BEM mesh data. |
| mne_list_coil_def | Create the coil description file. This is run automatically at when the software is set up, see Creating the coil definition file. |
| mne_list_proj | List signal-space projection data from a fif file. |
| mne_list_source_space | List source space information in text format suitable for importing into Neuromag MRIlab, see Listing source space data. |
| mne_list_versions | List versions and compilation dates of MNE software modules, see Finding software versions. |
| mne_make_cor_set | Used by mne_setup_mri to create fif format MRI description files from COR or mgh/mgz format MRI data, see Setting up the anatomical MR images for MRIlab. The mne_make_cor_set utility is described in Converting MRI data into the fif format. |
| mne_make_derivations | Create a channel derivation data file, see Creating a derivation file. |
| mne_make_eeg_layout | Make a topographical trace layout file using the EEG electrode locations from an actual measurement, see Creating a custom EEG layout. |
| mne_make_morph_maps | Precompute the mapping data needed for morphing between subjects, see Precomputing the morphing maps. |
| mne_make_uniform_stc | Create a spatially uniform stc file for testing purposes. |
| mne_mark_bad_channels | Update the list of unusable channels in a data file, see Designating bad channels: mne_mark_bad_channels. |
| mne_morph_labels | Morph label file definitions between subjects, see Morphing label data. |
| mne_organize_dicom | Organized DICOM MRI image files into directories, see Organizing MRI data into directories. |
| mne_prepare_bem_model | Perform the geometry calculations for BEM forward solutions, see Computing the BEM geometry data. |
| mne_process_stc | Manipulate stc files. |
| mne_raw2mat | Convert raw data into a Matlab file, see Converting raw data to Matlab format. |
| mne_rename_channels | Change the names and types of channels in a fif file, see Modifying channel names and types: mne_rename_channels. |
| mne_sensitivity_map | Compute a sensitivity map and output the result in a w-file, see Computing sensitivity maps. |
| mne_sensor_locations | Create a file containing the sensor locations in text format. |
| mne_show_fiff | List contents of a fif file, see Listing contents of a fif file. |
| mne_simu | Simulate MEG and EEG data, see Data simulator. |
| mne_smooth | Smooth a w or stc file. |
| mne_surf2bem | Create a fif file describing the triangulated compartment boundaries for the boundary-element model (BEM), see Creating the BEM meshes. |
| mne_toggle_skips | Change data skip tags in a raw file into ignored skips or vice versa. |
| mne_transform_points | Transform between MRI and MEG head coordinate frames, see Transforming locations. |
| mne_tufts2fiff | Convert EEG data from the Tufts University format to fif format, see Importing EEG data saved in the Tufts University format. |
| mne_view_manual | Starts a PDF reader to show this manual from its standard location. |
| mne_volume_data2mri | Convert volumetric data defined in a source space created with mne_volume_source_space into an MRI overlay, see Converting volumetric data into an MRI overlay. |
| mne_volume_source_space | Make a volumetric source space, see Creating a volumetric or discrete source space. |
| mne_watershed_bem | Do the segmentation for BEM using the watershed algorithm, see Using the watershed algorithm. |
The MNE software employs the fif file format whenever possible. New tags have been added to incorporate information specific to the calculation of cortically contained source estimates. FreeSurfer file formats are also employed when needed to represent cortical surface geometry data as well as spatiotemporal distribution of quantities on the surfaces. Of particular interest are the w files, which contain static overlay data on the cortical surface and stc files, which contain dynamic overlays (movies).
When command line examples are shown, the backslash character (\) indicates a continuation line. It is also valid in the shells. In most cases, however, you can easily fit the commands listed in this manual on one line and thus omit the backslashes. The order of options is irrelevant. Entries to be typed literally are shown like this . Italicized text indicates conceptual entries. For example, <*dir>* indicates a directory name.
In the description of interactive software modules the notation <menu>/<item> is often used to denotes menu selections. For example, File/Quit stands for the Quit button in the File menu.
All software modules employ the double-dash (--) option convention, i.e., the option names are preceded by two dashes.
Most of the programs have two common options to obtain general information:
—help
Prints concise usage information.
—version
Prints the program module name, version number, and compilation date.
The system-dependent location of the MNE Software will be here referred to by the environment variable MNE_ROOT. There are two scripts for setting up user environment so that the software can be used conveniently:
$MNE_ROOT/bin/mne_setup_sh
and
$MNE_ROOT/bin/mne_setup
compatible with the POSIX and csh/tcsh shells, respectively. Since the scripts set environment variables they should be ‘sourced’ to the present shell. You can find which type of a shell you are using by saying
echo $SHELL
If the output indicates a POSIX shell (bash or sh) you should issue the three commands:
export MNE_ROOT= <MNE> export MATLAB_ROOT= <Matlab> . $MNE_ROOT/bin/mne_setup_sh
with <MNE> replaced by the directory where you have installed the MNE software and <Matlab> is the directory where Matlab is installed. If you do not have Matlab, leave MATLAB_ROOT undefined. If Matlab is not available, the utilities mne_convert_mne_data , mne_epochs2mat , mne_raw2mat , and mne_simu will not work.
For csh/tcsh the corresponding commands are:
setenv MNE_ROOT <MNE> setenv MATLAB_ROOT <Matlab> source $MNE_ROOT/bin/mne_setup
For BEM mesh generation using the watershed algorithm or on the basis of multi-echo FLASH MRI data (see Creating the BEM meshes) and for accessing the tkmedit program from mne_analyze, see Working with the MRI viewer, the MNE software needs access to a FreeSurfer license and software. Therefore, to use these features it is mandatory that you set up the FreeSurfer environment as described in the FreeSurfer documentation.
The environment variables relevant to the MNE software are listed in Environment variables.
| Name of the variable | Description |
|---|---|
| MNE_ROOT | Location of the MNE software, see above. |
| FREESURFER_HOME | Location of the FreeSurfer software. Needed during FreeSurfer reconstruction and if the FreeSurfer MRI viewer is used with mne_analyze, see Working with the MRI viewer. |
| SUBJECTS_DIR | Location of the MRI data. |
| SUBJECT | Name of the current subject. |
| MNE_TRIGGER_CH_NAME | Name of the trigger channel in raw data, see Common options. |
| MNE_TRIGGER_CH_MASK | Mask to be applied to the trigger channel values, see Common options. |