C API Reference¶

Software components¶

Utilities¶

mne_analyze¶

Since mne_analyze is primarily an interactive analysis tool, there are only a few command-line options:

\---cd <*dir*>

Change to this directory before starting.

\---subject <*name*>

Specify the default subject name for surface loading.

\---digtrig <*name*>

Name of the digital trigger channel. The default value is ‘STI 014’. Underscores in the channel name will be replaced by spaces.

\---digtrigmask <*number*>

Mask to be applied to the raw data trigger channel values before considering them. This option is useful if one wants to set some bits in a don’t care state. For example, some finger response pads keep the trigger lines high if not in use, i.e., a finger is not in place. Yet, it is convenient to keep these devices permanently connected to the acquisition system. The number can be given in decimal or hexadecimal format (beginning with 0x or 0X). For example, the value 255 (0xFF) means that only the lowest order byte (usually trigger lines 1 - 8 or bits 0 - 7) will be considered.

\---visualizehpi

Start mne_analyze in the restricted head position visualization mode. For details, see Visualizing the head position.

\---dig <*filename*>

Specify a file containing the head shape digitization data. This option is only usable if the head position visualization position visualization mode has been first invoked with the –visualizehpi option.

\---hpi <*filename*>

Specify a file containing the transformation between the MEG device and head coordinate frames. This option is only usable if the head position visualization position visualization mode has been first invoked with the --visualizehpi option.

\---scalehead

In head position visualization mode, scale the average scalp surface according to the head surface digitization data before aligning them to the scalp surface. This option is recommended.

\---rthelmet

Use the room-temperature helmet surface instead of the MEG sensor surface when showing the relative position of the MEG sensors and the head in the head position visualization mode.

mne_average_estimates¶

This is a utility for averaging data in stc files. It requires that all stc files represent data on one individual’s cortical surface and contain identical sets of vertices. mne_average_estimates uses linear interpolation to resample data in time as necessary. The command line arguments are:

---desc <filenname>

Specifies the description file for averaging. The format of this file is described below.

mne_browse_raw¶

--cd <*dir*>

Change to this directory before starting.

--raw <*name*>

Specifies the raw data file to be opened. If a raw data file is not specified, an empty interactive browser will open.

--grad <*number*>

Apply software gradient compensation of the given order to the data loaded with the --raw option. This option is effective only for data acquired with the CTF and 4D Magnes MEG systems. If orders different from zero are requested for Neuromag data, an error message appears and data are not loaded. Any compensation already existing in the file can be undone or changed to another order by using an appropriate --grad options. Possible orders are 0 (No compensation), 1 - 3 (CTF data), and 101 (Magnes data). This applies only to the data file loaded by specifying the --raw option. For interactive data loading, the software gradient compensation is specified in the corresponding file selection dialog, see Open.

--filtersize <*size*>

Adjust the length of the FFT to be applied in filtering. The number will be rounded up to the next power of two. If the size is \(N\), the corresponding length of time is \(N/f_s\), where \(f_s\) is the sampling frequency of your data. The filtering procedure includes overlapping tapers of length \(N/2\) so that the total FFT length will actually be \(2N\). This value cannot be changed after the program has been started.

--highpass <*value/Hz*>

Highpass filter frequency limit. If this is too low with respect to the selected FFT length and, the data will not be highpass filtered. It is best to experiment with the interactive version to find the lowest applicable filter for your data. This value can be adjusted in the interactive version of the program. The default is 0, i.e., no highpass filter apart from that used during the acquisition will be in effect.

--highpassw <*value/Hz*>

The width of the transition band of the highpass filter. The default is 6 frequency bins, where one bin is \(f_s / (2N)\). This value cannot be adjusted in the interactive version of the program.

--lowpass <*value/Hz*>

Lowpass filter frequency limit. This value can be adjusted in the interactive version of the program. The default is 40 Hz.

--lowpassw <*value/Hz*>

The width of the transition band of the lowpass filter. This value can be adjusted in the interactive version of the program. The default is 5 Hz.

--eoghighpass <*value/Hz*>

Highpass filter frequency limit for EOG. If this is too low with respect to the selected FFT length and, the data will not be highpass filtered. It is best to experiment with the interactive version to find the lowest applicable filter for your data. This value can be adjusted in the interactive version of the program. The default is 0, i.e., no highpass filter apart from that used during the acquisition will be in effect.

--eoghighpassw <*value/Hz*>

The width of the transition band of the EOG highpass filter. The default is 6 frequency bins, where one bin is \(f_s / (2N)\). This value cannot be adjusted in the interactive version of the program.

--eoglowpass <*value/Hz*>

Lowpass filter frequency limit for EOG. This value can be adjusted in the interactive version of the program. The default is 40 Hz.

--eoglowpassw <*value/Hz*>

The width of the transition band of the EOG lowpass filter. This value can be adjusted in the interactive version of the program. The default is 5 Hz.

--filteroff

Do not filter the data. This initial value can be changed in the interactive version of the program.

--digtrig <*name*>

Name of the composite digital trigger channel. The default value is ‘STI 014’. Underscores in the channel name will be replaced by spaces.

--digtrigmask <*number*>

Mask to be applied to the trigger channel values before considering them. This option is useful if one wants to set some bits in a don’t care state. For example, some finger response pads keep the trigger lines high if not in use, i.e., a finger is not in place. Yet, it is convenient to keep these devices permanently connected to the acquisition system. The number can be given in decimal or hexadecimal format (beginning with 0x or 0X). For example, the value 255 (0xFF) means that only the lowest order byte (usually trigger lines 1 - 8 or bits 0 - 7) will be considered.

--allowmaxshield

Allow loading of unprocessed Elekta-Neuromag data with MaxShield on. These kind of data should never be used for source localization without further processing with Elekta-Neuromag software.

--deriv <*name*>

Specifies the name of a derivation file. This overrides the use of a standard derivation file, see Load derivations.

--sel <*name*>

Specifies the channel selection file to be used. This overrides the use of the standard channel selection files, see Selection.

mne_compute_mne¶

This program is gradually becoming obsolete. All of its functions will be eventually included to mne_make_movie, see Producing movies and snapshots. 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.

--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 \(\lambda = ^1/_{\text{SNR}}\). 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 \(\chi_2^3\) statistic instead of the F statistic. This is simply accomplished by multiplying the F statistic by three.

--sqrtF

Take the square root of the \(\chi_2^3\) 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) identical. The value at each source location is the \(L_1\) 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 \(L_2\) 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 Predicted data.

--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.

mne_compute_raw_inverse¶

--in <*filename*>

Specifies the input data file. This can be either an evoked data file or a raw data file.

--bmin <*time/ms*>

Specifies the starting time of the baseline. In order to activate baseline correction, both --bmin and --bmax options must be present. This option applies to evoked data only.

--bmax <*time/ms*>

Specifies the finishing time of the baseline. This option applies to evoked data only.

--set <*number*>

The data set (condition) number to load. This is the sequential number of the condition. You can easily see the association by looking at the condition list in mne_analyze when you load the file.

--inv <*name*>

Load the inverse operator decomposition from here.

--nave <*value*>

Specifies the effective number of averaged epochs in the input data, \(L_{eff}\), as discussed in Effective number of averages. If the input data file is one produced by mne_browse_raw or mne_process_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 along the guidelines given in Effective number of averages. This is accomplished either by employing this flag or by adjusting the number of averages in the data file with help of the utility mne_change_nave .

--snr <*value*>

An estimate for the amplitude SNR. The regularization parameter will be set as \(\lambda^2 = 1/SNR^2\). The default value is SNR = 1. Automatic selection of the regularization parameter is currently not supported.

--spm

Calculate the dSPM instead of the expected current value.

--picknormalcomp

The components of the estimates corresponding to directions tangential with the cortical mantle are zeroed out.

--mricoord

Provide source locations and orientations in the MRI coordinate frame instead of the default head coordinate frame.

--label <*name*>

Specifies a label file to process. For each label file, the values of the computed estimates stored in a fif file. For more details, see Implementation details. The label files are produced by tksurfer or mne_analyze 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> .fif and -rh- <data type> .fif , respectively. <data type> equals 'mne ‘ for expected current data and 'spm ‘ for dSPM data. For raw data, _raw.fif is employed instead of .fif . The output files are stored in the same directory as the label files.

--labelselout

Produces additional label files for each label processed, containing only those vertices within the input label which correspond to available source space vertices in the inverse operator. These files have the same name as the original label except that -lh and -rh are replaced by -sel-lh and -sel-rh , respectively.

--align_z

Instructs the program to try to align the waveform signs within the label. For more information, see Implementation details. This flag will not have any effect if the inverse operator has been computed with the strict orientation constraint active.

--labeldir <*directory*>

All previous --label options will be ignored when this option is encountered. For each label in the directory, the output file defined with the --out option will contain a summarizing waveform which is the average of the waveforms in the vertices of the label. The --labeldir option implies --align_z and --picknormalcomp options.

--orignames

This option is used with the --labeldir option, above. With this option, the output file channel names will be the names of the label files, truncated to 15 characters, instead of names containing the vertex numbers.

--out <*name*>

Required with --labeldir . This is the output file for the data.

--extra <*name*>

By default, the output includes the current estimate signals and the digital trigger channel, see --digtrig option, below. With the --extra option, a custom set of additional channels can be included. The extra channel text file should contain the names of these channels, one channel name on each line. With this option present, the digital trigger channel is not included unless specified in the extra channel file.

--noextra

No additional channels will be included with this option present.

--digtrig <*name*>

Name of the composite digital trigger channel. The default value is ‘STI 014’. Underscores in the channel name will be replaced by spaces.

--split <*size/MB*>

Specifies the maximum size of the raw data files saved. By default, the output is split into files which are just below 2 GB so that the fif file maximum size is not exceed.

mne_convert_mne_data¶

This utility allows the conversion of various fif files related to the MNE computations to other formats. The two principal purposes of this utility are to facilitate development of new analysis approaches with Matlab and conversion of the forward model and noise covariance matrix data into evoked-response type fif files, which can be accessed and displayed with the Neuromag source modelling software.

The command-line options recognized by mne_convert_mne_data are:

--fwd <*name*>

Specity the name of the forward solution file to be converted. Channels specified with the --bad option will be excluded from the file.

--fixed

Convert the forward solution to the fixed-orientation mode before outputting the converted file. With this option only the field patterns corresponding to a dipole aligned with the estimated cortex surface normal are output.

--surfsrc

When outputting a free-orientation forward model (three orthogonal dipole components present) rotate the dipole coordinate system at each source node so that the two tangential dipole components are output first, followed by the field corresponding to the dipole aligned with the estimated cortex surface normal. The orientation of the first two dipole components in the tangential plane is arbitrarily selected to create an orthogonal coordinate system.

--noiseonly

When creating a ‘measurement’ fif file, do not output a forward model file, just the noise-covariance matrix.

--senscov <*name*>

Specifies the fif file containing a sensor covariance matrix to be included with the output. If no other input files are specified only the covariance matrix is output

--srccov <*name*>

Specifies the fif file containing the source covariance matrix to be included with the output. Only diagonal source covariance files can be handled at the moment.

--bad <*name*>

Specifies the name of the file containing the names of the channels to be omitted, one channel name per line. This does not affect the output of the inverse operator since the channels have been already selected when the file was created.

--fif

Output the forward model and the noise-covariance matrix into ‘measurement’ fif files. The forward model files are tagged with <modalities> -meas-fwd.fif and the noise-covariance matrix files with <modalities> -meas-cov.fif . Here, modalities is -meg if MEG is included, -eeg if EEG is included, and -meg-eeg if both types of signals are present. The inclusion of modalities is controlled by the --meg and --eeg options.

--mat

Output the data into MATLAB mat files. This is the default. The forward model files are tagged with <modalities> -fwd.mat forward model and noise-covariance matrix output, with -inv.mat for inverse operator output, and with -inv-meas.mat for combined inverse operator and measurement data output, respectively. The meaning of <modalities> is the same as in the fif output, described above.

--tag <*name*>

By default, all variables in the matlab output files start with mne\_. This option allows to change this prefix to <name> _.

--meg

Include MEG channels from the forward solution and noise-covariance matrix.

--eeg

Include EEG channels from the forward solution and noise-covariance matrix.

--inv <*name*>

Output the inverse operator data from the specified file into a mat file. The source and noise covariance matrices as well as active channels have been previously selected when the inverse operator was created with mne_inverse_operator . Thus the options --meg , --eeg , --senscov , --srccov , --noiseonly , and --bad do not affect the output of the inverse operator.

--meas <*name*>

Specifies the file containing measurement data to be output together with the inverse operator. The channels corresponding to the inverse operator are automatically selected from the file if --inv . option is present. Otherwise, the channel selection given with --sel option will be taken into account.

--set <*number*>

Select the data set to be output from the measurement file.

--bmin <*value/ms*>

Specifies the baseline minimum value setting for the measurement signal output.

--bmax <*value/ms*>

Specifies the baseline maximum value setting for the measurement signal output.

mne_do_forward_solution¶

This utility accepts the following options:

--subject <*subject*>

Defines the name of the subject. This can be also accomplished by setting the SUBJECT environment variable.

--src <*name*>

Source space name to use. This option overrides the --spacing option. The source space is searched first from the current working directory and then from $SUBJECTS_DIR/ <subject> /bem. The source space file must be specified exactly, including the fif extension.

--spacing <*spacing/mm*>  or ``ico- <number or “oct-“ <*number>“

This is an alternate way to specify the name of the source space file. For example, if --spacing 6 is given on the command line, the source space files searched for are./<subject> -6-src.fif and $SUBJECTS_DIR/$SUBJECT/ bem/<subject> -6-src.fif. The first file found is used. Spacing defaults to 7 mm.

--bem <*name*>

Specifies the BEM to be used. The name of the file can be any of <name> , <name> -bem.fif, <name> -bem-sol.fif. The file is searched for from the current working directory and from bem . If this option is omitted, the most recent BEM file in the bem directory is used.

--mri <*name*>

The name of the MRI description file containing the MEG/MRI coordinate transformation. This file was saved as part of the alignment procedure outlined in Aligning coordinate frames. The file is searched for from the current working directory and from mri/T1-neuromag/sets . The search order for MEG/MRI coordinate transformations is discussed below.

--trans        <*name*>

The name of a text file containing the 4 x 4 matrix for the coordinate transformation from head to mri coordinates, see below. If the option --trans is present, the --mri option is not required. The search order for MEG/MRI coordinate transformations is discussed below.

--meas <*name*>

This file is the measurement fif file or an off-line average file produced thereof. It is recommended that the average file is employed for evoked-response data and the original raw data file otherwise. This file provides the MEG sensor locations and orientations as well as EEG electrode locations as well as the coordinate transformation between the MEG device coordinates and MEG head-based coordinates.

--fwd <*name*>

This file will contain the forward solution as well as the coordinate transformations, sensor and electrode location information, and the source space data. A name of the form <name> -fwd.fif is recommended. If this option is omitted the forward solution file name is automatically created from the measurement file name and the source space name.

--destdir <*directory*>

Optionally specifies a directory where the forward solution will be stored.

--mindist <*dist/mm*>

Omit source space points closer than this value to the inner skull surface. Any source space points outside the inner skull surface are automatically omitted. The use of this option ensures that numerical inaccuracies for very superficial sources do not cause unexpected effects in the final current estimates. Suitable value for this parameter is of the order of the size of the triangles on the inner skull surface. If you employ the seglab software to create the triangulations, this value should be about equal to the wish for the side length of the triangles.

--megonly

Omit EEG forward calculations.

--eegonly

Omit MEG forward calculations.

--all

Compute the forward solution for all vertices on the source space.

--overwrite

Overwrite the possibly existing forward model file.

--help

Show usage information for the script.

The MEG/MRI transformation is determined by the following search sequence:

• If the --mri option was present, the file is looked for literally as specified, in the directory of the measurement file specified with the --meas option, and in the directory $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets. If the file is not found, the script exits with an error message.
• If the --trans option was present, the file is looked up literally as specified. If the file is not found, the script exists with an error message.
• If neither --mri nor --trans option was not present, the following default search sequence is engaged:
  • The .fif ending in the measurement file name is replaced by -trans.fif . If this file is present, it will be used.
  • The newest file whose name ends with -trans.fif in the directory of the measurement file is looked up. If such a file is present, it will be used.
  • The newest file whose name starts with COR- in directory $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets is looked up. If such a file is present, it will be used.
  • If all the above searches fail, the script exits with an error message.

This search sequence is designed to work well with the MEG/MRI transformation files output by mne_analyze , see Coordinate frame alignment. It is recommended that -trans.fif file saved with the Save default and Save… options in the mne_analyze alignment dialog are used because then the $SUBJECTS_DIR/$SUBJECT directory will be composed of files which are dependent on the subjects’s anatomy only, not on the MEG/EEG data to be analyzed.

defined so that if the augmented location vectors in MRI head and MRI coordinate systems are denoted by \(r_{head}[x_{head}\ y_{head}\ z_{head}\ 1]\) and \(r_{MRI}[x_{MRI}\ y_{MRI}\ z_{MRI}\ 1]\), respectively,

mne_do_inverse_operator¶

--fwd <*name of the forward solution file*>

This is the forward solution file produced in the computations step described in Computing the forward solution.

--meg

Employ MEG data in the inverse calculation. If neither --meg nor --eeg is set only MEG channels are included.

--eeg

Employ EEG data in the inverse calculation. If neither --meg nor --eeg is set only MEG channels are included.

--fixed

Use fixed source orientations normal to the cortical mantle. By default, the source orientations are not constrained. If --fixed is specified, the --loose flag is ignored.

--loose <*amount*>

Use a ‘loose’ orientation constraint. This means that the source covariance matrix entries corresponding to the current component normal to the cortex are set equal to one and the transverse components are set to <amount> . Recommended value of amount is 0.1…0.6.

--depth

Employ depth weighting with the standard settings. For details, see Depth weighting and Inverse-operator decomposition.

--bad <*name*>

Specifies a text file to designate bad channels, listed one channel name (like MEG 1933) on each line of the file. Be sure to include both noisy and flat (non-functioning) channels in the list. If bad channels were designated using mne_mark_bad_channels in the measurement file which was specified with the --meas option when the forward solution was computed, the bad channel information will be automatically included. Also, any bad channel information in the noise-covariance matrix file will be included.

--noisecov <*name*>

Name of the noise-covariance matrix file computed with one of the methods described in Computing the noise-covariance matrix. By default, the script looks for a file whose name is derived from the forward solution file by replacing its ending - <anything> -fwd.fif by -cov.fif . If this file contains a projection operator, which will automatically attached to the noise-covariance matrix by mne_browse_raw and mne_process_raw , no --proj option is necessary because mne_inverse_operator will automatically include the projectors from the noise-covariance matrix file. For backward compatibility, –senscov can be used as a synonym for –noisecov.

--noiserank <*value*>

Specifies the rank of the noise covariance matrix explicitly rather than trying to reduce it automatically. This option is sheldom needed,

--megreg <*value*>

Regularize the MEG part of the noise-covariance matrix by this amount. Suitable values are in the range 0.05…0.2. For details, see Regularization of the noise-covariance matrix.

--eegreg <*value*>

Like --megreg but applies to the EEG channels.

--diagnoise

Omit the off-diagonal terms of the noise covariance matrix. This option is irrelevant to most users.

--fmri <*name*>

With help of this w file, an a priori weighting can be applied to the source covariance matrix. The source of the weighting is usually fMRI but may be also some other data, provided that the weighting can be expressed as a scalar value on the cortical surface, stored in a w file. It is recommended that this w file is appropriately smoothed (see About smoothing) in mne_analyze , tksurfer or with mne_smooth_w to contain nonzero values at all vertices of the triangular tessellation of the cortical surface. The name of the file given is used as a stem of the w files. The actual files should be called <name> -lh.pri and <name> -rh.pri for the left and right hemisphere weight files, respectively. The application of the weighting is discussed in fMRI-guided estimates.

--fmrithresh <*value*>

This option is mandatory and has an effect only if a weighting function has been specified with the --fmri option. If the value is in the a priori files falls below this value at a particular source space point, the source covariance matrix values are multiplied by the value specified with the --fmrioff option (default 0.1). Otherwise it is left unchanged.

--fmrioff <*value*>

The value by which the source covariance elements are multiplied if the a priori weight falls below the threshold set with --fmrithresh , see above.

--srccov <*name*>

Use this diagonal source covariance matrix. By default the source covariance matrix is a multiple of the identity matrix. This option is irrelevant to most users.

--proj <*name*>

Include signal-space projection information from this file.

--inv <*name*>

Save the inverse operator decomposition here. By default, the script looks for a file whose name is derived from the forward solution file by replacing its ending -fwd.fif by <options> -inv.fif , where <options> includes options --meg, --eeg, and --fixed with the double dashes replaced by single ones.

--destdir <*directory*>

Optionally specifies a directory where the inverse operator will be stored.

mne_forward_solution¶

--src <*name*>

Source space name to use. The name of the file must be specified exactly, including the directory. Typically, the source space files reside in $SUBJECTS_DIR/$SUBJECT/bem.

--bem <*name*>

Specifies the BEM to be used. These files end with bem.fif or bem-sol.fif and reside in $SUBJECTS_DIR/$SUBJECT/bem. The former file contains only the BEM surface information while the latter files contain the geometry information precomputed with mne_prepare_bem_model, see Computing the BEM geometry data. If precomputed geometry is not available, the linear collocation solution will be computed by mne_forward_solution .

--origin <*x/mm*> : <*x/mm*> : <*z/mm*>

Indicates that the sphere model should be used in the forward calculations. The origin is specified in MEG head coordinates unless the --mricoord option is present. The MEG sphere model solution computed using the analytical Sarvas formula. For EEG, an approximative solution described in

--eegmodels <*name*>

This option is significant only if the sphere model is used and EEG channels are present. The specified file contains specifications of the EEG sphere model layer structures as detailed in The EEG sphere model definition file. If this option is absent the file $HOME/.mne/EEG_models will be consulted if it exists.

--eegmodel <*model name*>

Specifies the name of the sphere model to be used for EEG. If this option is missing, the model Default will be employed, see The EEG sphere model definition file.

--eegrad <*radius/mm*>

Specifies the radius of the outermost surface (scalp) of the EEG sphere model, see The EEG sphere model definition file. The default value is 90 mm.

--eegscalp

Scale the EEG electrode locations to the surface of the outermost sphere when using the sphere model.

--accurate

Use accurate MEG sensor coil descriptions. This is the recommended choice. More information

--fixed

Compute the solution for sources normal to the cortical mantle only. This option should be used only for surface-based and discrete source spaces.

--all

Compute the forward solution for all vertices on the source space.

--label <*name*>

Compute the solution only for points within the specified label. Multiple labels can be present. The label files should end with -lh.label or -rh.label for left and right hemisphere label files, respectively. If --all flag is present, all surface points falling within the labels are included. Otherwise, only decimated points with in the label are selected.

--mindist <*dist/mm*>

Omit source space points closer than this value to the inner skull surface. Any source space points outside the inner skull surface are automatically omitted. The use of this option ensures that numerical inaccuracies for very superficial sources do not cause unexpected effects in the final current estimates. Suitable value for this parameter is of the order of the size of the triangles on the inner skull surface. If you employ the seglab software to create the triangulations, this value should be about equal to the wish for the side length of the triangles.

--mindistout <*name*>

Specifies a file name to contain the coordinates of source space points omitted due to the --mindist option.

--mri <*name*>

The name of the MRI description file containing the MEG/MRI coordinate transformation. This file was saved as part of the alignment procedure outlined in Aligning coordinate frames. These files typically reside in $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets .

--trans        <*name*>

The name of a text file containing the 4 x 4 matrix for the coordinate transformation from head to mri coordinates. With --trans, --mri option is not required.

--notrans

The MEG/MRI coordinate transformation is taken as the identity transformation, i.e., the two coordinate systems are the same. This option is useful only in special circumstances. If more than one of the --mri , --trans , and --notrans options are specified, the last one remains in effect.

--mricoord

Do all computations in the MRI coordinate system. The forward solution matrix is not affected by this option if the source orientations are fixed to be normal to the cortical mantle. If all three source components are included, the forward three source orientations parallel to the coordinate axes is computed. If --mricoord is present, these axes correspond to MRI coordinate system rather than the default MEG head coordinate system. This option is useful only in special circumstances.

--meas <*name*>

This file is the measurement fif file or an off-line average file produced thereof. It is recommended that the average file is employed for evoked-response data and the original raw data file otherwise. This file provides the MEG sensor locations and orientations as well as EEG electrode locations as well as the coordinate transformation between the MEG device coordinates and MEG head-based coordinates.

--fwd <*name*>

This file will contain the forward solution as well as the coordinate transformations, sensor and electrode location information, and the source space data. A name of the form <name>-fwd.fif is recommended.

--meg

Compute the MEG forward solution.

--eeg

Compute the EEG forward solution.

--grad

Include the derivatives of the fields with respect to the dipole position coordinates to the output, see Field derivatives.

mne_inverse_operator¶

--meg

Employ MEG data in the calculation of the estimates.

--eeg

Employ EEG data in the calculation of the estimates. Note: The EEG computations have not been thoroughly tested at this time.

--fixed

Use fixed source orientations normal to the cortical mantle. By default, the source orientations are not constrained.

--loose <amount>

Employ a loose orientation constraint (LOC). This means that the source covariance matrix entries corresponding to the current component normal to the cortex are set equal to one and the transverse components are set to <amount> . Recommended value of amount is 0.2…0.6.

--loosevar <amount>

Use an adaptive loose orientation constraint. This option can be only employed if the source spaces included in the forward solution have the patch information computed, see Setting up the source space.

--fwd <name>

Specifies the name of the forward solution to use.

--noisecov <name>

Specifies the name of the noise-covariance matrix to use. If this file contains a projection operator, attached by mne_browse_raw and mne_process_raw, no additional projection vectors can be added with the --proj option. For backward compatibility, --senscov can be used as a synonym for --noisecov.

--noiserank <value>

Specifies the rank of the noise covariance matrix explicitly rather than trying to reduce it automatically. This option is seldom needed,

--gradreg <value>

Regularize the planar gradiometer section (channels for which the unit of measurement is T/m) of the noise-covariance matrix by the given amount. The value is restricted to the range 0…1. For details, see Regularization of the noise-covariance matrix.

--magreg <value>

Regularize the magnetometer and axial gradiometer section (channels for which the unit of measurement is T) of the noise-covariance matrix by the given amount. The value is restricted to the range 0…1. For details, see Regularization of the noise-covariance matrix.

--eegreg <value>

Regularize the EEG section of the noise-covariance matrix by the given amount. The value is restricted to the range 0…1. For details, see Regularization of the noise-covariance matrix.

--diagnoise

Omit the off-diagonal terms from the noise-covariance matrix in the computations. This may be useful if the amount of signal-free data has been insufficient to calculate a reliable estimate of the full noise-covariance matrix.

--srccov <name>

Specifies the name of the diagonal source-covariance matrix to use. By default the source covariance matrix is a multiple of the identity matrix. This option can be employed to incorporate the fMRI constraint. The software to create a source-covariance matrix file from fMRI data will be provided in a future release of this software package.

--depth

Employ depth weighting. For details, see Depth weighting.

--weightexp <value>

This parameter determines the steepness of the depth weighting function (default = 0.8). For details, see Depth weighting.

--weightlimit <value>

Maximum relative strength of the depth weighting (default = 10). For details, see Depth weighting.

--fmri <name>

With help of this w file, an a priori weighting can be applied to the source covariance matrix. The source of the weighting is usually fMRI but may be also some other data, provided that the weighting can be expressed as a scalar value on the cortical surface, stored in a w file. It is recommended that this w file is appropriately smoothed (see About smoothing) in mne_analyze , tksurfer or with mne_smooth_w to contain nonzero values at all vertices of the triangular tessellation of the cortical surface. The name of the file given is used as a stem of the w files. The actual files should be called <name> -lh.pri and <name> -rh.pri for the left and right hemsphere weight files, respectively. The application of the weighting is discussed in fMRI-guided estimates.

--fmrithresh <value>

This option is mandatory and has an effect only if a weighting function has been specified with the --fmri option. If the value is in the a priori files falls below this value at a particular source space point, the source covariance matrix values are multiplied by the value specified with the --fmrioff option (default 0.1). Otherwise it is left unchanged.

--fmrioff <value>

The value by which the source covariance elements are multiplied if the a priori weight falls below the threshold set with --fmrithresh , see above.

--bad <name>

A text file to designate bad channels, listed one channel name on each line of the file. If the noise-covariance matrix specified with the --noisecov option contains projections, bad channel lists can be included only if they specify all channels containing non-zero entries in a projection vector. For example, bad channels can usually specify all magnetometers or all gradiometers since the projection vectors for these channel types are completely separate. Similarly, it is possible to include MEG data only or EEG data only by using only one of --meg or --eeg options since the projection vectors for MEG and EEG are always separate.

--surfsrc

Use a source coordinate system based on the local surface orientation at the source location. By default, the three dipole components are pointing to the directions of the x, y, and z axis of the coordinate system employed in the forward calculation (usually the MEG head coordinate frame). This option changes the orientation so that the first two source components lie in the plane normal to the surface normal at the source location and the third component is aligned with it. If patch information is available in the source space, the normal is the average patch normal, otherwise the vertex normal at the source location is used. If the --loose or --loosevar option is employed, --surfsrc is implied.

--exclude <name>

Exclude the source space points defined by the given FreeSurfer ‘label’ file from the source reconstruction. This is accomplished by setting the corresponding entries in the source-covariance matrix equal to zero. The name of the file should end with -lh.label if it refers to the left hemisphere and with -rh.label if it lists points in the right hemisphere, respectively.

--proj <name>

Include signal-space projection (SSP) information from this file. For information on SSP, see The Signal-Space Projection (SSP) method. If the projections are present in the noise-covariance matrix, the --proj option is not allowed.

--csd

Compute the inverse operator for surface current densities instead of the dipole source amplitudes. This requires the computation of patch statistics for the source space. Since this computation is time consuming, it is recommended that the patch statistics are precomputed and the source space file containing the patch information is employed already when the forward solution is computed, see Setting up the source space and Computing the forward solution. For technical details of the patch information, please consult Cortical patch statistics. This option is considered experimental at the moment.

--inv <name>

Save the inverse operator decomposition here.

mne_make_movie¶

mne_make_source_space¶

--subject <name>

Name of the subject.

--morph <name>

Name of the subject to morph the source space to.

--spacing <dist>

Approximate source space spacing in mm.

--ico <grade>

Use the subdivided icosahedron or octahedron in downsampling instead of the –spacing option.

--oct <grade>

Same as –ico -grade.

--surf <names>

Surface file names (separated by colons)

--src <name>

Name of the output file.

mne_process_raw¶

--cd <*dir*>

Change to this directory before starting.

--raw <*name*>

Specifies the raw data file to be opened. This option is required.

--grad <*number*>

Apply software gradient compensation of the given order to the data loaded with the --raw option. This option is effective only for data acquired with the CTF and 4D Magnes MEG systems. If orders different from zero are requested for Neuromag data, an error message appears and data are not loaded. Any compensation already existing in the file can be undone or changed to another order by using an appropriate --grad options. Possible orders are 0 (No compensation), 1 - 3 (CTF data), and 101 (Magnes data). The same compensation will be applied to all loaded data files.

--filtersize <*size*>

Adjust the length of the FFT to be applied in filtering. The number will be rounded up to the next power of two. If the size is \(N\), the corresponding length of time is \(N/f_s\), where \(f_s\) is the sampling frequency of your data. The filtering procedure includes overlapping tapers of length \(N/2\) so that the total FFT length will actually be \(2N\). This value cannot be changed after the program has been started.

--highpass <*value/Hz*>

Highpass filter frequency limit. If this is too low with respect to the selected FFT length and, the data will not be highpass filtered. It is best to experiment with the interactive version to find the lowest applicable filter for your data. This value can be adjusted in the interactive version of the program. The default is 0, i.e., no highpass filter apart from that used during the acquisition will be in effect.

--highpassw <*value/Hz*>

The width of the transition band of the highpass filter. The default is 6 frequency bins, where one bin is \(f_s / (2N)\). This value cannot be adjusted in the interactive version of the program.

--lowpass <*value/Hz*>

Lowpass filter frequency limit. This value can be adjusted in the interactive version of the program. The default is 40 Hz.

--lowpassw <*value/Hz*>

The width of the transition band of the lowpass filter. This value can be adjusted in the interactive version of the program. The default is 5 Hz.

--eoghighpass <*value/Hz*>

Highpass filter frequency limit for EOG. If this is too low with respect to the selected FFT length and, the data will not be highpass filtered. It is best to experiment with the interactive version to find the lowest applicable filter for your data. This value can be adjusted in the interactive version of the program. The default is 0, i.e., no highpass filter apart from that used during the acquisition will be in effect.

--eoghighpassw <*value/Hz*>

The width of the transition band of the EOG highpass filter. The default is 6 frequency bins, where one bin is \(f_s / (2N)\). This value cannot be adjusted in the interactive version of the program.

--eoglowpass <*value/Hz*>

Lowpass filter frequency limit for EOG. This value can be adjusted in the interactive version of the program. The default is 40 Hz.

--eoglowpassw <*value/Hz*>

The width of the transition band of the EOG lowpass filter. This value can be adjusted in the interactive version of the program. The default is 5 Hz.

--filteroff

Do not filter the data. This initial value can be changed in the interactive version of the program.

--digtrig <*name*>

Name of the composite digital trigger channel. The default value is ‘STI 014’. Underscores in the channel name will be replaced by spaces.

--digtrigmask <*number*>

Mask to be applied to the trigger channel values before considering them. This option is useful if one wants to set some bits in a don’t care state. For example, some finger response pads keep the trigger lines high if not in use, i.e., a finger is not in place. Yet, it is convenient to keep these devices permanently connected to the acquisition system. The number can be given in decimal or hexadecimal format (beginning with 0x or 0X). For example, the value 255 (0xFF) means that only the lowest order byte (usually trigger lines 1 - 8 or bits 0 - 7) will be considered.

--proj <*name*>

Specify the name of the file of the file containing a signal-space projection (SSP) operator. If --proj options are present the data file is not consulted for an SSP operator. The operator corresponding to average EEG reference is always added if EEG data are present.

--projon

Activate the projections loaded. One of the options --projon or --projoff must be present on the mne_processs_raw command line.

--projoff

Deactivate the projections loaded. One of the options --projon or --projoff must be present on the mne_processs_raw command line.

--makeproj

Estimate the noise subspace from the data and create a new signal-space projection operator instead of using one attached to the data file or those specified with the --proj option. The following eight options define the parameters of the noise subspace estimation. More information on the signal-space projection can be found in The Signal-Space Projection (SSP) method.

--projevent <*no*>

Specifies the events which identify the time points of interest for projector calculation. When this option is present, --projtmin and --projtmax are relative to the time point of the event rather than the whole raw data file.

--projtmin <*time/s*>

Specify the beginning time for the calculation of the covariance matrix which serves as the basis for the new SSP operator. This option is required with --projevent and defaults to the beginning of the raw data file otherwise. This option is effective only if --makeproj or --saveprojtag options are present.

--projtmax <*time/s*>

Specify the ending time for the calculation of the covariance matrix which serves as the basis for the new SSP operator. This option is required with --projevent and defaults to the end of the raw data file otherwise. This option is effective only if --makeproj or --saveprojtag options are present.

--projngrad <*number*>

Number of SSP components to include for planar gradiometers (default = 5). This value is system dependent. For example, in a well-shielded quiet environment, no planar gradiometer projections are usually needed.

--projnmag <*number*>

Number of SSP components to include for magnetometers / axial gradiometers (default = 8). This value is system dependent. For example, in a well-shielded quiet environment, 3 - 4 components are need while in a noisy environment with light shielding even more than 8 components may be necessary.

--projgradrej <*value/ fT/cm*>

Rejection limit for planar gradiometers in the estimation of the covariance matrix frfixom which the new SSP operator is derived. The default value is 2000 fT/cm. Again, this value is system dependent.

--projmagrej <*value/ fT*>

Rejection limit for planar gradiometers in the estimation of the covariance matrix from which the new SSP operator is derived. The default value is 3000 fT. Again, this value is system dependent.

--saveprojtag <*tag*>

This option defines the names of files to hold the SSP operator. If this option is present the --makeproj option is implied. The SSP operator file name is formed by removing the trailing .fif or _raw.fif from the raw data file name by appending <tag> .fif to this stem. Recommended value for <tag> is -proj .

--saveprojaug

Specify this option if you want to use the projection operator file output in the Elekta-Neuromag Signal processor (graph) software.

--eventsout <*name*>

List the digital trigger channel events to the specified file. By default, only transitions from zero to a non-zero value are listed. If multiple raw data files are specified, an equal number of --eventsout options should be present. If the file name ends with .fif, the output will be in fif format, otherwise a text event file will be output.

--allevents

List all transitions to file specified with the --eventsout option.

--events <*name*>

Specifies the name of a fif or text format event file (see Event files) to be associated with a raw data file to be processed. If multiple raw data files are specified, the number of --events options can be smaller or equal to the number of raw data files. If it is equal, the event filenames will be associated with the raw data files in the order given. If it is smaller, the remaining raw data files for which an event file is not specified will not have an event file associated with them. The event file format is recognized from the file name: if it ends with .fif , the file is assumed to be in fif format, otherwise a text file is expected.

--ave <*name*>

Specifies the name of an off-line averaging description file. For details of the format of this file, please consult Description files for off-line averaging. If multiple raw data files are specified, the number of --ave options can be smaller or equal to the number of raw data files. If it is equal, the averaging description file names will be associated with the raw data files in the order given. If it is smaller, the last description file will be used for the remaining raw data files.

--saveavetag <*tag*>

If this option is present and averaging is evoked with the --ave option, the outfile and logfile options in the averaging description file are ignored. Instead, trailing .fif or _raw.fif is removed from the raw data file name and <tag> .fif or <tag> .log is appended to create the output and log file names, respectively.

--gave <*name*>

If multiple raw data files are specified as input and averaging is requested, the grand average over all data files will be saved to <name> .

--cov <*name*>

Specify the name of a description file for covariance matrix estimation. For details of the format of this file, please see Description files for covariance matrix estimation. If multiple raw data files are specified, the number of --cov options can be smaller or equal to the number of raw data files. If it is equal, the averaging description file names will be associated with the raw data files in the order given. If it is smaller, the last description file will be used for the remaining raw data files.

--savecovtag <*tag*>

If this option is present and covariance matrix estimation is evoked with the --cov option, the outfile and logfile options in the covariance estimation description file are ignored. Instead, trailing .fif or _raw.fif is removed from the raw data file name and <tag> .fif or <tag> .log is appended to create the output and log file names, respectively. For compatibility with other MNE software scripts, --savecovtag -cov is recommended.

--savehere

If the --saveavetag and --savecovtag options are used to generate the file output file names, the resulting files will go to the same directory as raw data by default. With this option the output files will be generated in the current working directory instead.

--gcov <*name*>

If multiple raw data files are specified as input and covariance matrix estimation is requested, the grand average over all data files will be saved to <name> . The details of the covariance matrix estimation are given in Covariance matrix estimation.

--save <*name*>

Save a filtered and optionally down-sampled version of the data file to <name> . If multiple raw data files are specified, an equal number of --save options should be present. If <filename> ends with .fif or _raw.fif , these endings are deleted. After these modifications, _raw.fif is inserted after the remaining part of the file name. If the file is split into multiple parts (see --split option below), the additional parts will be called <name> - <number> _raw.fif

--split <*size/MB*>

Specifies the maximum size of the raw data files saved with the --save option. By default, the output is split into files which are just below 2 GB so that the fif file maximum size is not exceed.

--anon

Do not include any subject information in the output files created with the --save option.

--decim <*number*>

The data are decimated by this factor before saving to the file specified with the --save option. For decimation to succeed, the data must be lowpass filtered to less than third of the sampling frequency effective after decimation.

mne_redo_file¶

Usage: mne_redo_file file-to-redo

mne_redo_file_nocwd¶

Usage: mne_redo_file_nocwd file-to-redo

mne_setup_forward_model¶

--subject <*subject*>

Defines the name of the subject. This can be also accomplished by setting the SUBJECT environment variable.

--surf

Use the FreeSurfer surface files instead of the default ASCII triangulation files. Please consult Setting up the head surface triangulation files for the standard file naming scheme.

--noswap

Traditionally, the vertices of the triangles in ‘tri’ files have been ordered so that, seen from the outside of the triangulation, the vertices are ordered in clockwise fashion. The fif files, however, employ the more standard convention with the vertices ordered counterclockwise. Therefore, mne_setup_forward_model by default reverses the vertex ordering before writing the fif file. If, for some reason, you have counterclockwise-ordered tri files available this behavior can be turned off by defining --noswap . When the fif file is created, the vertex ordering is checked and the process is aborted if it is incorrect after taking into account the state of the swapping. Should this happen, try to run mne_setup_forward_model again including the --noswap flag. In particular, if you employ the seglab software to create the triangulations (see Creating the BEM meshes), the --noswap flag is required. This option is ignored if --surf is specified

--ico <*number*>

This option is relevant (and required) only with the --surf option and if the surface files have been produced by the watershed algorithm. The watershed triangulations are isomorphic with an icosahedron, which has been recursively subdivided six times to yield 20480 triangles. However, this number of triangles results in a long computation time even in a workstation with generous amounts of memory. Therefore, the triangulations have to be decimated. Specifying --ico 4 yields 5120 triangles per surface while --ico 3 results in 1280 triangles. The recommended choice is --ico 4 .

--homog

Use a single compartment model (brain only) instead a three layer one (scalp, skull, and brain). Only the inner_skull.tri triangulation is required. This model is usually sufficient for MEG but invalid for EEG. If you are employing MEG data only, this option is recommended because of faster computation times. If this flag is specified, the options --brainc , --skullc , and --scalpc are irrelevant.

--brainc <*conductivity/ S/m*>

Defines the brain compartment conductivity. The default value is 0.3 S/m.

--skullc <*conductivity/ S/m*>

Defines the skull compartment conductivity. The default value is 0.006 S/m corresponding to a conductivity ratio 1/50 between the brain and skull compartments.

--scalpc <*conductivity/ S/m*>

Defines the brain compartment conductivity. The default value is 0.3 S/m.

--innershift <*value/mm*>

Shift the inner skull surface outwards along the vertex normal directions by this amount.

--outershift <*value/mm*>

Shift the outer skull surface outwards along the vertex normal directions by this amount.

--scalpshift <*value/mm*>

Shift the scalp surface outwards along the vertex normal directions by this amount.

--nosol

Omit the BEM model geometry dependent data preparation step. This can be done later by running mne_setup_forward_model without the --nosol option.

--model <*name*>

Name for the BEM model geometry file. The model will be created into the directory bem as <name>- bem.fif . If this option is missing, standard model names will be used (see below).

mne_setup_mri¶

This command sets up the directories subjects/$SUBJECT/mri/T1-neuromag and subjects/$SUBJECT/mri/brain-neuromag .

mne_setup_source_space¶

--subject <*name*>

Name of the subject in SUBJECTS_DIR. In the absence of this option, the SUBJECT environment variable will be consulted. If it is not defined, mne_setup_source_space exits with an error.

--morph <*name*>

Name of a subject in SUBJECTS_DIR. If this option is present, the source space will be first constructed for the subject defined by the –subject option or the SUBJECT environment variable and then morphed to this subject. This option is useful if you want to create a source spaces for several subjects and want to directly compare the data across subjects at the source space vertices without any morphing procedure afterwards. The drawback of this approach is that the spacing between source locations in the “morph” subject is not going to be as uniform as it would be without morphing.

--surf <*name1*>: <*name2*>:...

FreeSurfer surface file names specifying the source surfaces, separated by colons.

--spacing <*spacing/mm*>

Specifies the approximate grid spacing of the source space in mm.

--ico <*number*>

Instead of using the traditional method for cortical surface decimation it is possible to create the source space using the topology of a recursively subdivided icosahedron ( <number> > 0) or an octahedron ( <number> < 0). This method uses the cortical surface inflated to a sphere as a tool to find the appropriate vertices for the source space. The benefit of the --ico option is that the source space will have triangulation information between the decimated vertices included, which some future versions of MNE software may be able to utilize. The number of triangles increases by a factor of four in each subdivision, starting from 20 triangles in an icosahedron and 8 triangles in an octahedron. Since the number of vertices on a closed surface is \(n_{vert} = (n_{tri} + 4) / 2\), the number of vertices in the k th subdivision of an icosahedron and an octahedron are \(10 \cdot 4^k +2\) and \(4_{k + 1} + 2\), respectively. The recommended values for <number> and the corresponding number of source space locations are listed in Table 3.1.

--all

Include all nodes to the output. The active dipole nodes are identified in the fif file by a separate tag. If tri files were used as input the output file will also contain information about the surface triangulation. This option is always recommended to include complete information.

--src <*name*>

Output file name. Use a name <dir>/<name>-src.fif

mne_show_environment¶

Usage: mne_show_environment files

mne_add_patch_info¶

mne_add_to_meas_info¶

Add new data to meas info.

--add <name>

The file to add.

--dest <name>

the destination file.

mne_add_triggers¶

mne_annot2labels¶

The utility mne_annot2labels converts cortical parcellation data into a set of labels. The parcellation data are read from the directory $SUBJECTS_DIR/$SUBJECT/label and the resulting labels are written to the current directory. mne_annot2labels requires that the environment variable $SUBJECTS_DIR is set. The command line options for mne_annot2labels are:

--subject  <*name*>

Specifies the name of the subject. If this option is not present the $SUBJECT environment variable is consulted. If the subject name cannot be determined, the program quits.

--parc  <*name*>

Specifies the parcellation name to convert. The corresponding parcellation file names will be $SUBJECTS_DIR/$SUBJECT/label/ <hemi> h. <name> .annot where <hemi> is l or r for the left and right hemisphere, respectively.

mne_anonymize¶

Depending no the settings during acquisition in the Elekta-Neuromag EEG/MEG systems the data files may contain subject identifying information in unencrypted form. The utility mne_anonymize was written to clear tags containing such information from a fif file. Specifically, this utility removes the following tags from the fif file:

mne_anonymize recognizes the following command-line options:

--his

Remove the FIFF_SUBJ_HIS_ID tag as well, see above.

--file  <*name*>

Specifies the name of the file to be modified.

mne_average_forward_solutions¶

--fwd <*name*> :[ <*weight*> ]

Specifies a forward solution to include. If no weight is specified, 1.0 is assumed. In the averaging process the weights are divided by their sum. For example, if two forward solutions are averaged and their specified weights are 2 and 3, the average is formed with a weight of 2/5 for the first solution and 3/5 for the second one.

--out <*name*>

Specifies the output file which will contain the averaged forward solution.

mne_brain_vision2fiff¶

The utility mne_brain_vision2fiff was created to import BrainVision EEG data. This utility also helps to import the eXimia (Nexstim) TMS-compatible EEG system data to the MNE software. The utility uses an optional fif file containing the head digitization data to allow source modeling. The MNE Matlab toolbox contains the function fiff_write_dig_file to write a digitization file based on digitization data available in another format, see Matlab toolbox.

The command-line options of mne_brain_vision2fiff are:

--header <*name*>

The name of the BrainVision header file. The extension of this file is vhdr . The header file typically refers to a marker file (vmrk ) which is automatically processed and a digital trigger channel (STI 014) is formed from the marker information. The vmrk file is ignored if the --eximia option is present.

--dig <*name*>

The name of the fif file containing the digitization data.

--orignames

Use the original EEG channel labels. If this option is absent the EEG channels will be automatically renamed to EEG 001, EEG 002, etc.

--eximia

Interpret this as an eXimia data file. The first three channels will be thresholded and interpreted as trigger channels. The composite digital trigger channel will be composed in the same way as in the mne_kit2fiff utility. In addition, the fourth channel will be assigned as an EOG channel. This option is normally used by the mne_eximia2fiff script.

--split <*size/MB*>

Split the output data into several files which are no more than <size> MB. By default, the output is split into files which are just below 2 GB so that the fif file maximum size is not exceeded.

--out <*filename*>

Specifies the name of the output fif format data file. If <filename> ends with .fif or _raw.fif , these endings are deleted. After these modifications, _raw.fif is inserted after the remaining part of the file name. If the file is split into multiple parts, the additional parts will be called <name> - <number> _raw.fif .

mne_change_baselines¶

The utility mne_change_baselines computes baseline values and applies them to an evoked-response data file. The command-line options are:

--in  <*name*>

Specifies the input data file.

--set  <*number*>

The data set number to compute baselines from or to apply baselines to. If this option is omitted, all average data sets in the input file are processed.

--out  <*name*>

The output file.

--baselines  <*name*>

Specifies a text file which contains the baseline values to be applied. Each line should contain a channel name, colon, and the baseline value given in ‘native’ units (T/m, T, or V). If this option is encountered, the limits specified by previous --bmin and --bmax options will not have an effect.

--list  <*name*>

Specifies a text file to contain the baseline values. Listing is provided only if a specific data set is selected with the --set option.

--bmin  <*value/ms*>

Lower limit of the baseline. Effective only if --baselines option is not present. Both --bmin and --bmax must be present to compute the baseline values. If either --bmin or --bmax is encountered, previous --baselines option will be ignored.

--bmax  <*value/ms*>

Upper limit of the baseline.

mne_change_nave¶

Usage: mne_change_nave --nave <number> <meas file> ...

mne_check_eeg_locations¶

Some versions of the Neuromag acquisition software did not copy the EEG channel location information properly from the Polhemus digitizer information data block to the EEG channel information records if the number of EEG channels exceeds 60. The purpose of mne_check_eeg_locations is to detect this problem and fix it, if requested. The command-line options are:

--file  <*name*>

Specify the measurement data file to be checked or modified.

--dig  <*name*>

Name of the file containing the Polhemus digitizer information. Default is the data file name.

--fix

By default mne_check_eeg_locations only checks for missing EEG locations (locations close to the origin). With –fix mne_check_eeg_locations reads the Polhemus data from the specified file and copies the EEG electrode location information to the channel information records in the measurement file. There is no harm running mne_check_eeg_locations on a data file even if the EEG channel locations were correct in the first place.

mne_check_surface¶

This program just reads a surface file to check whether it is valid.

--surf <name>

The input file (FreeSurfer surface format).

--bem <name>

The input file (a BEM fif file)

--id <id>

Surface id to list (default : 4)

• 4 for outer skin (scalp) surface * 3 for outer skull surface * 1 for inner skull surface

--checkmore

Do more thorough testing

mne_collect_transforms¶

The utility mne_collect_transforms collects coordinate transform information from various sources and saves them into a single fif file. The coordinate transformations used by MNE software are summarized in Figure 5.1. The output of mne_collect_transforms may include all transforms referred to therein except for the sensor coordinate system transformations \(T_{s_1} \dotso T_{s_n}\). The command-line options are:

--meas <*name*>

Specifies a measurement data file which provides \(T_1\). A forward solution or an inverse operator file can also be specified as implied by Table 5.1.

--mri <*name*>

Specifies an MRI description or a standalone coordinate transformation file produced by mne_analyze which provides \(T_2\). If the --mgh option is not present mne_collect_transforms also tries to find \(T_3\), \(T_4\), \(T_-\), and \(T_+\) from this file.

--mgh <*name*>

An MRI volume volume file in mgh or mgz format. This file provides \(T_3\). The transformation \(T_4\) will be read from the talairach.xfm file referred to in the MRI volume. The fixed transforms \(T_-\) and \(T_+\) will also be created.

--out <*name*>

Specifies the output file. If this option is not present, the collected transformations will be output on screen but not saved.

mne_compensate_data¶

--in <*name*>

Specifies the input data file.

--out <*name*>

Specifies the output data file.

--grad <*number*>

Specifies the desired compensation grade in the output file. The value can be 1, 2, 3, or 101. The values starting from 101 will be used for 4D Magnes compensation matrices.

mne_copy_processing_history¶

In order for the inverse operator calculation to work correctly with data processed with the Elekta-Neuromag Maxfilter (TM) software, the so-called processing history block must be included in data files. Previous versions of the MNE Matlab functions did not copy processing history to files saved. As of March 30, 2009, the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enchanced to include these data to the output file as appropriate. If you have older raw data files created in Matlab from input which has been processed Maxfilter, it is necessary to copy the processing history block from the original to modified raw data file using the mne_copy_processing_history utility described below. The raw data processing programs mne_browse_raw and mne_process_raw have handled copying of the processing history since revision 2.5 of the MNE software.

mne_copy_processing_history is simple to use:

mne_copy_processing_history --from <from> --to <to> ,

where <from> is an original raw data file containing the processing history and <to> is a file output with older MNE Matlab routines. Be careful: this operation cannot be undone. If the <from> file does not have the processing history block or the <to> file already has it, the destination file remains unchanged.

mne_convert_dig_data¶

Converts Polhemus digitization data between different file formats. The input formats are:

fif

The standard format used in MNE. The digitization data are typically present in the measurement files.

hpts

A text format which is a translation of the fif format data, see The hpts format below.

elp

A text format produced by the Source Signal Imaging, Inc. software. For description of this “probe” format, see http://www.sourcesignal.com/formats_probe.html.

The data can be output in fif and hpts formats. Only the last command-line option specifying an input file will be honored. Zero or more output file options can be present on the command line.

The command-line options of mne_convert_dig_data are:

--fif <*name*>

Specifies the name of an input fif file.

--hpts <*name*>

Specifies the name of an input hpts file.

--elp <*name*>

Specifies the name of an input elp file.

--fifout <*name*>

Specifies the name of an output fif file.

--hptsout <*name*>

Specifies the name of an output hpts file.

--headcoord

The fif and hpts input files are assumed to contain data in the MNE head coordinate system, see The head and device coordinate systems. With this option present, the data are transformed to the MNE head coordinate system with help of the fiducial locations in the data. Use this option if this is not the case or if you are unsure about the definition of the coordinate system of the fif and hpts input data. This option is implied with elp input files. If this option is present, the fif format output file will contain the transformation between the original digitizer data coordinates the MNE head coordinate system.

mne_convert_lspcov¶

The utility mne_convert_lspcov converts a LISP-format noise-covariance file, produced by the Neuromag signal processor, graph into fif format.

The command-line options are:

--lspcov <*name*>

The LISP noise-covariance matrix file to be converted.

--meas <*name*>

A fif format measurement file used to assign channel names to the noise-covariance matrix elements. This file should have precisely the same channel order within MEG and EEG as the LISP-format covariance matrix file.

--out <*name*>

The name of a fif format output file. The file name should end with -cov.fif.text format output file. No information about the channel names is included. The covariance matrix file is listed row by row. This file can be loaded to MATLAB, for example

--outasc <*name*>

The name of a text format output file. No information about the channel names is included. The covariance matrix file is listed row by row. This file can be loaded to MATLAB, for example

mne_convert_ncov¶

The ncov file format was used to store the noise-covariance matrix file. The MNE software requires that the covariance matrix files are in fif format. The utility mne_convert_ncov converts ncov files to fif format.

The command-line options are:

--ncov <*name*>

The ncov file to be converted.

--meas <*name*>

A fif format measurement file used to assign channel names to the noise-covariance matrix elements. This file should have precisely the same channel order within MEG and EEG as the ncov file. Typically, both the ncov file and the measurement file are created by the now mature off-line averager, meg_average.

mne_convert_surface¶

The utility mne_convert_surface converts surface data files between different formats.

mne_cov2proj¶

mne_create_comp_data¶

--in <*name*>

Specifies the input text file containing the compensation data.

--kind <*value*>

The compensation type to be stored in the output file with the data. This value defaults to 101 for the Magnes compensation and does not need to be changed.

--out <*name*>

Specifies the output fif file containing the compensation channel weight matrix \(C_{(k)}\), see Applying software gradient compensation.

The format of the text-format compensation data file is:

<number of MEG helmet channels> <number of compensation channels included> <cname_1> <cname_2> … <name_1> <weights> <name_2> <weights> …

In the above <name_k> denote names of MEG helmet channels and <cname_k> those of the compensation channels, respectively. If the channel names contain spaces, they must be surrounded by quotes, for example, "MEG 0111" .

mne_ctf2fiff¶

--verbose

Produce a verbose listing of the conversion process to stdout.

--ds <*directory*>

Read the data from this directory

--omit <*filename*>

Read the names of channels to be omitted from this text file. Enter one channel name per line. The names should match exactly with those listed in the CTF data structures. By default, all channels are included.

--fif <*filename*>

The name of the output file. If the length of the raw data exceeds the 2-GByte fif file limit, several output files will be produced. These additional ‘extension’ files will be tagged with _001.fif , _002.fif , etc.

--evoked

Produce and evoked-response fif file instead of a raw data file. Each trial in the CTF data file is included as a separate category (condition). The maximum number of samples in each trial is limited to 25000.

--infoonly

Write only the measurement info to the output file, do not include data.

During conversion, the following files are consulted from the ds directory:

“ <name> .res4“

This file contains most of the header information pertaining the acquisition.

“ <name> .hc“

This file contains the HPI coil locations in sensor and head coordinates.

“ <name> .meg4“

This file contains the actual MEG data. If the data are split across several files due to the 2-GByte file size restriction, the ‘extension’ files are called <name> . <number> _meg4 .

“ <name> .eeg“

This is an optional input file containing the EEG electrode locations. More details are given below.

If the <name> .eeg file, produced from the Polhemus data file with CTF software, is present, it is assumed to contain lines with the format:

<number> <name> <x/cm> <y/cm> <z/cm>

The field <number> is a sequential number to be assigned to the converted data point in the fif file. <name> is either a name of an EEG channel, one of left , right , or nasion to indicate a fiducial landmark, or any word which is not a name of any channel in the data. If <name> is a name of an EEG channel available in the data, the location is included in the Polhemus data as an EEG electrode locations and inserted as the location of the EEG electrode. If the name is one of the fiducial landmark names, the point is included in the Polhemus data as a fiducial landmark. Otherwise, the point is included as an additional head surface points.

The standard eeg file produced by CTF software does not contain the fiducial locations. If desired, they can be manually copied from the pos file which was the source of the eeg file.

mne_ctf_dig2fiff¶

The input data to mne_ctf_dig2fiff is a text file, which contains the coordinates of the digitization points in centimeters. The first line should contain a single number which is the number of points listed in the file. Each of the following lines contains a sequential number of the point, followed by the three coordinates. mne_ctf_dig2fiff ignores any text following the \(z\) coordinate on each line. If the --numfids option is specified, the first three points indicate the three fiducial locations (1 = nasion, 2 = left auricular point, 3 = right auricular point). Otherwise, the input file must end with three lines beginning with left , right , or nasion to indicate the locations of the fiducial landmarks, respectively.

The command-line options for mne_ctf_dig2fiff are:

--dig <*name*>

Specifies the input data file in CTF output format.

--numfids

Fiducial locations are numbered instead of labeled, see above.

--hpts <*name*>

Specifies the output hpts file. The format of this text file is described in The hpts format.

--fif <*name*>

Specifies the output fif file.

mne_dicom_essentials¶

Print essential information about a dicom file.

--in <name>

The input file.

mne_edf2fiff¶

The mne_edf2fiff allows conversion of EEG data from EDF, EDF+, and BDF formats to the fif format. Documentation for these three input formats can be found at:

EDF:

http://www.edfplus.info/specs/edf.html

EDF+:

http://www.edfplus.info/specs/edfplus.html

BDF:

http://www.biosemi.com/faq/file_format.htm

EDF (European Data Format) and EDF+ are 16-bit formats while BDF is a 24-bit variant of this format used by the EEG systems manufactured by a company called BioSemi.

None of these formats support electrode location information and head shape digitization information. Therefore, this information has to be provided separately. Presently hpts and elp file formats are supported to include digitization data. For information on these formats, see The hpts format and http://www.sourcesignal.com/formats_probe.html. Note that it is mandatory to have the three fiducial locations (nasion and the two auricular points) included in the digitization data. Using the locations of the fiducial points the digitization data are converted to the MEG head coordinate system employed in the MNE software, see The head and device coordinate systems. In the comparison of the channel names only the initial segment up to the first ‘-‘ (dash) in the EDF/EDF+/BDF channel name is significant.

The EDF+ files may contain an annotation channel which can be used to store trigger information. The Time-stamped Annotation Lists (TALs) on the annotation data can be converted to a trigger channel (STI 014) using an annotation map file which associates an annotation label with a number on the trigger channel. The TALs can be listed with the --listtal option, see below.

mne_epochs2mat¶

The utility mne_epochs2mat converts epoch data including all or selected channels from a raw data file to a simple binary file with an associated description file in Matlab mat file format. With help of the description file, a matlab program can easily read the epoch data from the simple binary file. Signal space projection and bandpass filtering can be optionally applied to the raw data prior to saving the epochs.

mne_evoked_data_summary¶

Print a summary of evoked-response data sets in a file (averages only).

--in <name>

The input file.

mne_eximia2fiff¶

Usage:

mne_eximia2fiff [--dig dfile ] [--orignames ] file1 file2 …

where file1 file2 … are eXimia nxe files and the --orignames option is passed on to mne_brain_vision2fiff. If you want to convert all data files in a directory, say

mne_eximia2fiff *.nxe

The optional file specified with the --dig option is assumed to contain digitizer data from the recording in the Nexstim format. The resulting fif data file will contain these data converted to the fif format as well as the coordinate transformation between the eXimia digitizer and MNE head coordinate systems.

mne_fit_sphere_to_surf¶

mne_fix_mag_coil_types¶

The purpose of mne_fix_mag_coil_types is to change coil type 3022 to 3024 in the MEG channel definition records in the data files specified on the command line.

As shown in Tables 5.2 and 5.3, the Neuromag Vectorview systems can contain magnetometers with two different coil sizes (coil types 3022 and 3023 vs. 3024). The systems incorporating coils of type 3024 were introduced last. At some sites the data files have still defined the magnetometers to be of type 3022 to ensure compatibility with older versions of Neuromag software. In the MNE software as well as in the present version of Neuromag software coil type 3024 is fully supported. Therefore, it is now safe to upgrade the data files to use the true coil type.

If the --magnes option is specified, the 4D Magnes magnetometer coil type (4001) is changed to 4D Magnes gradiometer coil type (4002). Use this option always and only if your Magnes data comes from a system with axial gradiometers instead of magnetometers. The fif converter included with the Magnes system does not assign the gradiometer coil type correctly.

mne_fix_stim14¶

Some earlier versions of the Neuromag acquisition software had a problem with the encoding of the eighth bit on the digital stimulus channel STI 014. This problem has been now fixed. Old data files can be fixed with mne_fix_stim14 , which takes raw data file names as arguments. mne_fix_stim14 also changes the calibration of STI 014 to unity. If the encoding of STI 014 is already correct, running mne_fix_stim14 will not have any effect on the raw data.

In newer Neuromag Vectorview systems with 16-bit digital inputs the upper two bytes of the samples may be incorrectly set when stimulus input 16 is used and the data are acquired in the 32-bit mode. This problem can be fixed by running mne_fix_stim14 on a raw data file with the --32 option:

mne_fix_stim14 --32 <raw data file>

In this case, the correction will be applied to the stimulus channels ‘STI101’ and ‘STI201’.

mne_flash_bem¶

--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.

mne_insert_4D_comp¶

Import Magnes WH3600 reference channel data from a text file.

--in <name>

The name of the fif file containing the helmet data.

--ref <name>

The name of the text file containing the reference channel data.

--out <name>

The output fif file.

mne_kit2fiff¶

The utility mne_kit2fiff was created in collaboration with Alec Maranz and Asaf Bachrach to import their MEG data acquired with the 160-channel KIT MEG system to MNE software.

To import the data, the following input files are mandatory:

• The Polhemus data file (elp file) containing the locations of the fiducials and the head-position indicator (HPI) coils. These data are usually given in the CTF/4D head coordinate system. However, mne_kit2fiff does not rely on this assumption. This file can be exported directly from the KIT system.
• A file containing the locations of the HPI coils in the MEG device coordinate system. These data are used together with the elp file to establish the coordinate transformation between the head and device coordinate systems. This file can be produced easily by manually editing one of the files exported by the KIT system.
• A sensor data file (sns file) containing the locations and orientations of the sensors. This file can be exported directly from the KIT system.

The following input files are optional:

• A head shape data file (hsp file) containing locations of additional points from the head surface. These points must be given in the same coordinate system as that used for the elp file and the fiducial locations must be within 1 mm from those in the elp file.
• A raw data file containing the raw data values, sample by sample, as text. If this file is not specified, the output fif file will only contain the measurement info block.

By default mne_kit2fiff includes the first 157 channels, assumed to be the MEG channels, in the output file. The compensation channel data are not converted by default but can be added, together with other channels, with the --type . The channels from 160 onwards are designated as miscellaneous input channels (MISC 001, MISC 002, etc.). The channel names and types of these channels can be afterwards changed with the mne_rename_channels utility. In addition, it is possible to synthesize the digital trigger channel (STI 014) from available analog trigger channel data, see the --stim option, below. The synthesized trigger channel data value at sample \(k\) will be:

where \(t_p(k)\) are the thresholded from the input channel data d_p(k):

The threshold value \(t\) can be adjusted with the --stimthresh option, see below.

mne_kit2fiff accepts the following command-line options:

--elp <*filename*>

The name of the file containing the locations of the fiducials and the HPI coils. This option is mandatory.

--hsp <*filename*>

The name of the file containing the locations of the fiducials and additional points on the head surface. This file is optional.

--sns <*filename*>

The name of file containing the sensor locations and orientations. This option is mandatory.

--hpi <*filename*>

The name of a text file containing the locations of the HPI coils in the MEG device coordinate frame, given in millimeters. The order of the coils in this file does not have to be the same as that in the elp file. This option is mandatory.

--raw <*filename*>

Specifies the name of the raw data file. If this file is not specified, the output fif file will only contain the measurement info block.

--sfreq <*value/Hz*>

The sampling frequency of the data. If this option is not specified, the sampling frequency defaults to 1000 Hz.

--lowpass <*value/Hz*>

The lowpass filter corner frequency used in the data acquisition. If not specified, this value defaults to 200 Hz.

--highpass <*value/Hz*>

The highpass filter corner frequency used in the data acquisition. If not specified, this value defaults to 0 Hz (DC recording).

--out <*filename*>

Specifies the name of the output fif format data file. If this file is not specified, no output is produced but the elp , hpi , and hsp files are processed normally.

--stim <*chs*>

Specifies a colon-separated list of numbers of channels to be used to synthesize a digital trigger channel. These numbers refer to the scanning order channels as listed in the sns file, starting from one. The digital trigger channel will be the last channel in the file. If this option is absent, the output file will not contain a trigger channel.

--stimthresh <*value*>

The threshold value used when synthesizing the digital trigger channel, see above. Defaults to 1.0.

--add <*chs*>

Specifies a colon-separated list of numbers of channels to include between the 157 default MEG channels and the digital trigger channel. These numbers refer to the scanning order channels as listed in the sns file, starting from one.

mne_list_bem¶

The utility mne_list_bem outputs the BEM meshes in text format. The default output data contains the x, y, and z coordinates of the vertices, listed in millimeters, one vertex per line.

The command-line options are:

--bem <*name*>

The BEM file to be listed. The file name normally ends with -bem.fif or -bem-sol.fif .

--out <*name*>

The output file name.

--id <*number*>

Identify the surface to be listed. The surfaces are numbered starting with the innermost surface. Thus, for a three-layer model the surface numbers are: 4 = scalp, 3 = outer skull, 1 = inner skull Default value is 4.

--gdipoli

List the surfaces in the format required by Thom Oostendorp’s gdipoli program. This is also the default input format for mne_surf2bem .

--meters

List the surface coordinates in meters instead of millimeters.

--surf

Write the output in the binary FreeSurfer format.

--xfit

Write a file compatible with xfit. This is the same effect as using the options --gdipoli and --meters together.

mne_list_coil_def¶

List available coil definitions.

--in <def>

Validate a coil definition file.

--out <name>

List the coil definitions to this file (default: stdout).

--type <type>

Coil type to list.

mne_list_proj¶

--in <name>

Input file.

--ascin <name>

Input file.

--exclude <name>

Exclude these channels from the projection (set entries to zero).

--chs <name>

Specify a file which contains a channel selection for the output (useful for graph)

--asc <name>

Text output.

--fif <name>

Fif output.

--lisp <name>

Lisp output.

mne_list_source_space¶

The utility mne_list_source_space outputs the source space information into text files suitable for loading into the Neuromag MRIlab software.

--src <*name*>

The source space to be listed. This can be either the output from mne_make_source_space (*src.fif), output from the forward calculation (*fwd.fif), or the output from the inverse operator decomposition (*inv.fif).

--mri <*name*>

A file containing the transformation between the head and MRI coordinates is specified with this option. This file can be either a Neuromag MRI description file, the output from the forward calculation (*fwd.fif), or the output from the inverse operator decomposition (*inv.fif). If this file is included, the output will be in head coordinates. Otherwise the source space will be listed in MRI coordinates.

--dip <*name*>

Specifies the ‘stem’ for the Neuromag text format dipole files to be output. Two files will be produced: <stem> -lh.dip and <stem> -rh.dip. These correspond to the left and right hemisphere part of the source space, respectively. This source space data can be imported to MRIlab through the File/Import/Dipoles menu item.

--pnt <*name*>

Specifies the ‘stem’ for Neuromag text format point files to be output. Two files will be produced: <stem> -lh.pnt and <stem> -rh.pnt. These correspond to the left and right hemisphere part of the source space, respectively. This source space data can be imported to MRIlab through the File/Import/Strings menu item.

--exclude <*name*>

Exclude the source space points defined by the given FreeSurfer ‘label’ file from the output. The name of the file should end with -lh.label if it refers to the left hemisphere and with -rh.label if it lists points in the right hemisphere, respectively.

--include <*name*>

Include only the source space points defined by the given FreeSurfer ‘label’ file to the output. The file naming convention is the same as described above under the --exclude option. Are ‘include’ labels are processed before the ‘exclude’ labels.

--all

Include all nodes in the output files instead of only those active in the source space. Note that the output files will be huge if this option is active.

mne_list_versions¶

The utility mne_list_versions lists version numbers and compilation dates of all software modules that provide this information. This administration utility is located in $MNE_ROOT/bin/admin , The output from mne_list_versions or output of individual modules with --version option is useful when bugs are reported to the developers of MNE software.

mne_make_cor_set¶

The utility mne_make_cor_set creates a fif format MRI description file optionally including the MRI data using FreeSurfer MRI volume data as input. The command-line options are:

--dir <*directory*>

Specifies a directory containing the MRI volume in COR format. Any previous --mgh options are cancelled when this option is encountered.

--withdata

Include the pixel data to the output file. This option is implied with the --mgh option.

--mgh <*name*>

An MRI volume volume file in mgh or mgz format. The --withdata option is implied with this type of input. Furthermore, the \(T_3\) transformation, the Talairach transformation \(T_4\) from the talairach.xfm file referred to in the MRI volume, and the the fixed transforms \(T_-\) and \(T_+\) will added to the output file. For definition of the coordinate transformations, see MEG/EEG and MRI coordinate systems.

--talairach <*name*>

Take the Talairach transform from this file instead of the one specified in mgh/mgz files.

--out <*name*>

Specifies the output file, which is a fif-format MRI description file.

mne_make_derivations¶

mne_make_eeg_layout¶

mne_make_morph_maps¶

Prepare the mapping data for subject-to-subject morphing.

--redo

Recompute the morphing maps even if they already exist.

--from <subject>

Compute morphing maps from this subject.

--to <subject>

Compute morphing maps to this subject.

--all

Do all combinations. If this is used without either --from or --to options, morphing maps for all possible combinations are computed. If --from or --to is present, only maps between the specified subject and all others are computed.

mne_make_uniform_stc¶

The output will have a time range from -100 to 300 ms. There will be one cycle of 5-Hz sine wave, with the peaks at 50 and 150 ms

--src <name>

Source space to use.

--stc <name>

Stc file to produce.

--maxval <value>

Maximum value (at 50 ms, default 10).

--all

Include all points to the output files.

mne_mark_bad_channels¶

This utility adds or replaces information about unusable (bad) channels. The command line options are:

--bad  <*filename*>

Specify a text file containing the names of the bad channels, one channel name per line. The names of the channels in this file must match those in the data file exactly. If this option is missing, the bad channel information is cleared.

<*data file name*>

The remaining arguments are taken as data file names to be modified.

mne_morph_labels¶

Morph label files from one brain to another.

--from <*subject*>

Name of the subject for which the labels were originally defined.

--to <*subject*>

Name of the subject for which the morphed labels should be created.

--labeldir <*directory*>

A directory containing the labels to morph.

--prefix <prefix>

Adds <prefix> in the beginning of the output label names. A dash will be inserted between <prefix> and the rest of the name.

--smooth <number>

Apply smoothing with the indicated number of iteration steps (see About smoothing) to the labels before morphing them. This is advisable because otherwise the resulting labels may have little holes in them since the morphing map is not a bijection. By default, two smoothsteps are taken.

As the labels are morphed, a directory with the name of the subject specified with the --to option is created under the directory specified with --labeldir to hold the morphed labels.

mne_organize_dicom¶

mne_prepare_bem_model¶

--bem <*name*>

Specify the name of the file containing the triangulations of the BEM surfaces and the conductivities of the compartments. The standard ending for this file is -bem.fif and it is produced either with the utility mne_surf2bem (Creating the BEM meshes) or the convenience script mne_setup_forward_model, see Setting up the boundary-element model.

--sol <*name*>

Specify the name of the file containing the triangulation and conductivity information together with the BEM geometry matrix computed by mne_prepare_bem_model . The standard ending for this file is -bem-sol.fif .

--method <*approximation method*>

Select the BEM approach. If <approximation method> is constant , the BEM basis functions are constant functions on each triangle and the collocation points are the midpoints of the triangles. With linear , the BEM basis functions are linear functions on each triangle and the collocation points are the vertices of the triangulation. This is the preferred method to use. The accuracy will be the same or better than in the constant collocation approach with about half the number of unknowns in the BEM equations.

mne_process_stc¶

--stc <name>

Specify the stc file to process.

--out <name>

Specify a stc output file name.

--outasc <name>

Specify a text output file name.

--scaleto <scale>

Scale the data so that the maximum is this value.

--scaleby <scale>

Multiply the values by this.

mne_raw2mat¶

The utility mne_raw2mat converts all or selected channels from a raw data file to a Matlab mat file. In addition, this utility can provide information about the raw data file so that the raw data can be read directly from the original fif file using Matlab file I/O routines.

mne_rename_channels¶

Sometimes it is necessary to change the names types of channels in MEG/EEG data files. Such situations include:

• Designating an EEG as an EOG channel. For example, the EOG channels are not recognized as such in the fif files converted from CTF data files.
• Changing the name of the digital trigger channel of interest to STI 014 so that mne_browse_raw and mne_process_raw will recognize the correct channel without the need to specify the --digtrig option or the MNE_TRIGGER_CH_NAME environment variable every time a data file is loaded.

The utility mne_rename_channels was designed to meet the above needs. It recognizes the following command-line options:

--fif  <*name*>

Specifies the name of the data file to modify.

--alias  <*name*>

Specifies the text file which contains the modifications to be applied, see below.

--revert

Reverse the roles of old and new channel names in the alias file.

Each line in the alias file contains the old name and new name for a channel, separated by a colon. The old name is a name of one of the channels presently in the file and the new name is the name to be assigned to it. The old name must match an existing channel name in the file exactly. The new name may be followed by another colon and a number which is the channel type to be assigned to this channel. The channel type options are listed below.

mne_sensitivity_map¶

mne_sensor_locations¶

--meas <name>

Measurement file.

--magonly

Magnetometers only.

--ell

Output sensor ellipsoids for MRIlab.

--dir

Output direction info as well.

--dev

Output in MEG device coordinates.

--out <name>

Name output file

mne_show_fiff¶

Using the utility mne_show_fiff it is possible to display information about the contents of a fif file to the standard output. The command line options for mne_show_fiff are:

--in  <*name*>

Specifies the fif file whose contents will be listed.

--verbose

Produce a verbose output. The data of most tags is included in the output. This excludes matrices and vectors. Only the first 80 characters of strings are listed unless the --long option is present.

--blocks

Only list the blocks (the tree structure) of the file. The tags within each block are not listed.

--indent  <*number*>

Number of spaces for indentation for each deeper level in the tree structure of the fif files. The default indentation is 3 spaces in terse and no spaces in verbose listing mode.

--long

List all data from string tags instead of the first 80 characters. This options has no effect unless the --verbose option is also present.

--tag  <*number*>

List only tags of this kind. Multiple --tag options can be specified to list several different kinds of data.

mne_show_fiff reads the explanations of tag kinds, block kinds, and units from $MNE_ROOT/share/mne/fiff_explanations.txt .

mne_simu¶

mne_smooth¶

Produce a smoothed version of a w or an stc file

--src <name>

The source space file.

--in <name>

The w or stc file to smooth.

--smooth <val>

Number of smoothsteps

mne_surf2bem¶

--surf <*name*>

Specifies a FreeSurfer binary format surface file. Before specifying the next surface (--surf or --tri options) details of the surface specification can be given with the options listed in Surface options.

--tri <*name*>

Specifies a text format surface file. Before specifying the next surface (--surf or --tri options) details of the surface specification can be given with the options listed in Surface options. The format of these files is described in Tessellation file format.

--check

Check that the surfaces are complete and that they do not intersect. This is a recommended option. For more information, see Topology checks.

--checkmore

In addition to the checks implied by the --check option, check skull and skull thicknesses. For more information, see Topology checks.

--fif <*name*>

The output fif file containing the BEM. These files normally reside in the bem subdirectory under the subject’s mri data. A name ending with -bem.fif is recommended.

mne_toggle_skips¶

Toggle skip tags on and off.

--raw <name>

The raw data file to process.

mne_transform_points¶

mne_tufts2fiff¶

--raw <*filename*>

Specifies the name of the raw data file to process.

--cal <*filename*>

The name of the calibration data file. If calibration data are missing, the calibration coefficients will be set to unity.

--elp <*filename*>

The name of the electrode location file. If this file is missing, the electrode locations will be unspecified. This file is in the “probe” file format used by the Source Signal Imaging, Inc. software. For description of the format, see http://www.sourcesignal.com/formats_probe.html. The fiducial marker locations, optional in the “probe” file format specification are mandatory for mne_tufts2fiff . Note that some other software packages may produce electrode-position files with the elp ending not conforming to the above specification.

mne_view_manual¶

This script shows you the manual in a PDF reader.

mne_volume_data2mri¶

With help of the mne_volume_source_space utility it is possible to create a source space which is defined within a volume rather than a surface. If the --mri option was used in mne_volume_source_space, the source space file contains an interpolator matrix which performs a trilinear interpolation into the voxel space of the MRI volume specified.

The purpose of the mne_volume_data2mri is to produce MRI overlay data compatible with FreeSurfer MRI viewers (in the mgh or mgz formats) from this type of w or stc files.

The command-line options are:

--src <*filename*>

The name of the volumetric source space file created with mne_volume_source_space . The source space must have been created with the --mri option, which adds the appropriate sparse trilinear interpolator matrix to the source space.

--w <*filename*>

The name of a w file to convert into an MRI overlay.

--stc <*filename*>

The name of the stc file to convert into an MRI overlay. If this file has many time frames, the output file may be huge. Note: If both -w and --stc are specified, -w takes precedence.

--scale <*number*>

Multiply the stc or w by this scaling constant before producing the overlay.

--out <*filename*>

Specifies the name of the output MRI overlay file. The name must end with either .mgh or .mgz identifying the uncompressed and compressed FreeSurfer MRI formats, respectively.

mne_volume_source_space¶

--surf <*name*>

Specifies a FreeSurfer surface file containing the surface which will be used as the boundary for the source space.

--bem <*name*>

Specifies a BEM file (ending in -bem.fif ). The inner skull surface will be used as the boundary for the source space.

--origin <*x/mm*> : <*y/mm*> : <*z/mm*>

If neither of the two surface options described above is present, the source space will be spherical with the origin at this location, given in MRI (RAS) coordinates.

--rad <*radius/mm*>

Specifies the radius of a spherical source space. Default value = 90 mm

--grid <*spacing/mm*>

Specifies the grid spacing in the source space.

--mindist <*distance/mm*>

Only points which are further than this distance from the bounding surface are included. Default value = 5 mm.

--exclude <*distance/mm*>

Exclude points that are closer than this distance to the center of mass of the bounding surface. By default, there will be no exclusion.

--mri <*name*>

Specifies a MRI volume (in mgz or mgh format). If this argument is present the output source space file will contain a (sparse) interpolation matrix which allows mne_volume_data2mri to create an MRI overlay file, see mne_volume_data2mri.

--pos <*name*>

Specifies a name of a text file containing the source locations and, optionally, orientations. Each line of the file should contain 3 or 6 values. If the number of values is 3, they indicate the source location, in millimeters. The orientation of the sources will be set to the z-direction. If the number of values is 6, the source orientation will be parallel to the vector defined by the remaining 3 numbers on each line. With --pos , all of the options defined above will be ignored. By default, the source position and orientation data are assumed to be given in MRI coordinates.

--head

If this option is present, the source locations and orientations in the file specified with the --pos option are assumed to be given in the MEG head coordinates.

--meters

Indicates that the source locations in the file defined with the --pos option are give in meters instead of millimeters.

--src <*name*>

Specifies the output file name. Use a name * <dir>/ <name>*-src.fif

--all

Include all vertices in the output file, not just those in use. This option is implied when the --mri option is present. Even with the --all option, only those vertices actually selected will be marked to be “in use” in the output source space file.

mne_watershed_bem¶

--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.