Difference between revisions of "Command Line Tools"
From MNE-CPP Wiki
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--version print version info. | --version print version info. | ||
− | == mne_forward_solution == | + | == Example == |
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+ | = mne_forward_solution = | ||
+ | == Usage == | ||
Calculate a forward solution | Calculate a forward solution | ||
--meg to compute the MEG forward solution | --meg to compute the MEG forward solution | ||
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--version print version info. | --version print version info. | ||
− | == | + | == Example== |
+ | = mne_show_fiff = | ||
+ | == Usage == | ||
List contents of a fif file to stdout | List contents of a fif file to stdout | ||
--in name The input file. | --in name The input file. | ||
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--help print this info. | --help print this info. | ||
--version print version info. | --version print version info. | ||
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+ | == Example == |
Revision as of 03:41, 8 March 2017
Contents
mne_dipole_fit
Usage
This is a program for sequential single dipole fitting.
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.
Example
mne_forward_solution
Usage
Calculate a forward solution
--meg to compute the MEG forward solution --eeg to compute the EEG forward solution --grad compute the gradient of the field with respect to the dipole coordinates as well --fixed to calculate only for the source orientation given by the surface normals --mricoord do calculations in MRI coordinates instead of head coordinates --accurate use more accurate coil definitions in MEG forward computation --src name specify the source space --label name label file to select the sources (can have multiple of these) --mri name take head/MRI coordinate transform from here (Neuromag MRI description file) --trans name take head/MRI coordinate transform from here (text file) --notrans head and MRI coordinate systems are identical. --meas name take MEG sensor and EEG electrode locations from here --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 rad/mm radius of the scalp surface to use in EEG sphere model (default : 90.0 mm) --mindist dist/mm minimum allowable distance of the sources from the inner skull surface. --mindistout name Output the omitted source space points here. --includeall Omit all source space checks --all calculate forward solution in all nodes instead the selected ones only. --fwd name save the solution here --help print this info. --version print version info.
Example
mne_show_fiff
Usage
List contents of a fif file to stdout
--in name The input file. --fif name Synonym for the above. --blocks Only list the blocks (the tree structure) --verbose Verbose output. --indent no Number of spaces to use in indentation (default -1 in terse and 0 in verbose output) --tag no Provide information about these tags (can have multiple of these). --long Print long strings in full? --help print this info. --version print version info.