FieldTrip

Note that this reference documentation is identical to the help that is displayed in Matlab when you type “help ft_prepare_sourcemodel”.

  FT_PREPARE_SOURCEMODEL constructs a source model, for example a 3-D grid or a
  cortical sheet. The source model that can be used for source reconstruction,
  beamformer scanning, linear estimation and MEG interpolation.
 
  Use as
    grid = prepare_prepare_sourcemodel(cfg)
 
  where the configuration structure contains the details on how the source
  model should be constructed.
 
  A source model can be constructed based on
    - regular 3D grid with explicit specification
    - regular 3D grid with specification of the resolution
    - regular 3D grid, based on segmented MRI, restricted to gray matter
    - regular 3D grid, based on a warped template grid, based on the MNI
        brain
    - surface grid based on brain surface from volume conductor
    - surface grid based on head surface from external file
    - using user-supplied grid positions, which can be regular or irregular
    - cortical sheet that was created in MNE or Freesurfer
  The approach that will be used depends on the configuration options that
  you specify.
 
  Configuration options for generating a regular 3-D grid
    cfg.grid.xgrid      = vector (e.g. -20:1:20) or 'auto' (default = 'auto')
    cfg.grid.ygrid      = vector (e.g. -20:1:20) or 'auto' (default = 'auto')
    cfg.grid.zgrid      = vector (e.g.   0:1:20) or 'auto' (default = 'auto')
    cfg.grid.resolution = number (e.g. 1 cm) for automatic grid generation
    cfg.sourceunits     = 'auto' (in which case the sourceunits default to the unit in the
                           sensor description), or 'mm'/'cm'/'dm'/'m'
 
  Configuration options for a predefined grid
    cfg.grid.pos        = N*3 matrix with position of each source
    cfg.grid.dim        = [Nx Ny Nz] vector with dimensions in case of 3-D grid (optional)
    cfg.grid.inside     = vector with indices of the sources inside the brain (optional)
    cfg.grid.outside    = vector with indices of the sources outside the brain (optional)
  The following fields are not used in this function, but will be copied along to the output
    cfg.grid.leadfield
    cfg.grid.filter or alternatively cfg.grid.avg.filter
    cfg.grid.subspace
    cfg.grid.lbex
 
  Configuration options for a warped MNI grid
    cfg.mri             = can be filename or MRI structure, containing the
                          individual anatomy
    cfg.grid.warpmni    = 'yes'
    cfg.grid.resolution = number (e.g. 6) of the resolution of the
                          template MNI grid, defined in mm
    cfg.grid.template   = specification of a template grid (grid
                          structure), or a
                          filename of a template grid (defined in MNI space),
                          either cfg.grid.resolution or cfg.grid.template needs
                          to be defined. If both are defined cfg.grid.template
                          prevails
    cfg.grid.nonlinear  = 'no' (or 'yes'), use non-linear normalization
    cfg.sourceunits     = 'auto'(in which case the sourceunits default to the unit in the
                           sensor description), or 'mm'/'cm'/'dm'/'m'
 
  Configuration options for cortex segmentation, i.e. for placing dipoles in grey matter
    cfg.mri           = can be filename, MRI structure or segmented MRI structure
    cfg.sourceunits   = 'auto' (in which case the sourceunits default to the unit in the
                        sensor description, if provided). otherwise it defaults to 'cm'
    cfg.threshold     = 0.1, relative to the maximum value in the segmentation
    cfg.smooth        = 5, smoothing in voxels
 
  Configuration options for reading a cortical sheet from file
    cfg.headshape     = string, should be a *.fif file
 
  Other configuration options
    cfg.vol          = volume conduction model
    cfg.grad         = gradiometer definition
    cfg.elec         = electrode definition
    cfg.grid.tight   = 'yes' or 'no' (default is automatic)
    cfg.inwardshift  = depth of the bounding layer for the source space, relative to the head model surface (default = 0)
    cfg.symmetry     = 'x', 'y' or 'z' symmetry for two dipoles, can be empty (default = [])
    cfg.headshape    = a filename containing headshape, a structure containing a
                       single triangulated boundary, or a Nx3 matrix with surface
                       points
 
  See also FT_PREPARE_LEADFIELD, FT_SOURCEANALYSIS, FT_DIPOLEFITTING, FT_MEGREALIGN