MNE Dipole Fit CLI
Command-line options
mne_dipole_fit
recognizes the following command-line options:
Input data:
--meas name specify an evoked-response data file
--set no evoked data set number to use (default: 1)
--bad name take bad channel list from here
Modality selection:
--meg employ MEG data in fitting
--eeg employ EEG data in fitting
Time scale selection:
--tmin time/ms specify the starting analysis time
--tmax time/ms specify the ending analysis time
--tstep time/ms specify the time step between frames (default 1/(sampling frequency))
--integ time/ms specify the time integration for each frame (default 0)
Preprocessing:
--bmin time/ms specify the baseline starting time (evoked data only)
--bmax time/ms specify the baseline ending time (evoked data only)
--proj name Load the linear projection from here
Multiple projections can be specified.
The data file will be automatically included, unless --noproj is present.
--noproj Do not load the projection from the data file, just those given with the --proj option.
Filtering (raw data only):
--filtersize size desired filter length (default = 4096)
--highpass val/Hz highpass corner (default = 0.0 Hz)
--lowpass val/Hz lowpass corner (default = 40.0 Hz)
--lowpassw val/Hz lowpass transition width (default = 5.0 Hz)
--filteroff do not filter the data
Noise specification:
--noise name take the noise-covariance matrix from here
--gradnoise val specify a gradiometer noise value in fT/cm
--magnoise val specify a gradiometer noise value in fT
--eegnoise val specify an EEG value in uV
NOTE: The above will be used only if --noise is missing
--diagnoise omit off-diagonal terms from the noise-covariance matrix
--reg amount Apply regularization to the noise-covariance matrix (same fraction for all channels).
--gradreg amount Apply regularization to the MEG noise-covariance matrix (planar gradiometers, default = 0.10).
--magreg amount Apply regularization to the EEG noise-covariance matrix (axial gradiometers and magnetometers, default = 0.10).
--eegreg amount Apply regularization to the EEG noise-covariance matrix (default = 0.10).
Forward model:
--mri name take head/MRI coordinate transform from here (Neuromag MRI description file)
--bem name BEM model name
--origin x:y:z/mm use a sphere model with this origin (head coordinates/mm)
--eegscalp scale the electrode locations to the surface of the scalp when using a sphere model
--eegmodels name read EEG sphere model specifications from here.
--eegmodel name name of the EEG sphere model to use (default : Default)
--eegrad val radius of the scalp surface to use in EEG sphere model (default : 90.0 mm)
--accurate use accurate coil definitions in MEG forward computation
Fitting parameters:
--guess name The source space of initial guesses.
If not present, the values below are used to generate the guess grid.
--guesssurf name Read the inner skull surface from this fif file to generate the guesses.
--guessrad value Radius of a spherical guess volume if neither of the above is present (default : 80.0 mm)
--exclude dist/mm Exclude points which are closer than this distance from the CM of the inner skull surface (default = 20.0 mm).
--mindist dist/mm Exclude points which are closer than this distance from the inner skull surface (default = 10.0 mm).
--grid dist/mm Source space grid size (default = 10.0 mm).
--magdip Fit magnetic dipoles instead of current dipoles.
Output:
--dip name xfit dip format output file name
--bdip name xfit bdip format output file name
General:
--gui Enables the gui.
--help print this info.
--version print version info.
Examples
mne_dipole_fit --meas ./MNE-sample-data/MEG/sample/sample_audvis-ave.fif --noise ./MNE-sample-data/MEG/sample/sample_audvis-cov.fif --bem ./MNE-sample-data/subjects/sample/bem/sample-5120-bem.fif --mri ./MNE-sample-data/MEG/sample/sample_audvis_raw-trans.fif --set 1 --meg --tmin 32 --tmax 148 --bmin -100 --bmax 0 --gui --dip ./MNE-sample-data/Result/dip-result.dat