Latest revision as of 16:40, 9 March 2017

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_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

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.

Example