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== mne_dipole_fit ==
 
== mne_dipole_fit ==
 +
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.
  
 
== mne_forward_solution ==
 
== mne_forward_solution ==

Revision as of 18:48, 7 March 2017

mne_dipole_fit

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.

mne_forward_solution

mne_show_fiff

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.
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