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= 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 K:/Git/mne-cpp/bin/MNE-sample-data/MEG/sample/sample_audvis-ave.fif --set 1 --meg --eeg --tmin 32 --tmax 148 --bmin -100 --bmax 0 --dip K:/Git/mne-cpp/bin/MNE-sample-data/Result/dip-result.dat --gui

= 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 ==