FieldTrip

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

  FT_VOLUMESEGMENT segments an anatomical MRI. The behaviour depends on the
  output requested. It can return probabilistic tissue maps of
  gray/white/csf compartments, a skull-stripped anatomy, or binary masks
  representing the brain surface, skull, or scalp surface.
 
  Use as
    segment = ft_volumesegment(cfg, mri)
  where the input mri should be a single anatomical volume that was for
  example read with FT_READ_MRI. You can also provide an already segmented
  volume as input for the purpose of creating a binary mask.
 
  The configuration structure can contain
    cfg.output      = 'tpm' (default), 'brain', 'skull', 'skullstrip', 'scalp', or any
                         combination of these in a cell-array
    cfg.spmversion  = 'spm8' (default) or 'spm2'
    cfg.template    = filename of the template anatomical MRI (default is the 'T1.nii' 
                      (spm8) or 'T1.mnc' (spm2) in the (spm-directory)/templates/)
    cfg.name        = string for output filename
    cfg.write       = 'no' or 'yes' (default = 'no'),
                      writes the probabilistic tissue maps to SPM compatible analyze (spm2),
                      or nifti (spm8) files,
                      with the suffix (spm2)
                      _seg1, for the gray matter segmentation
                      _seg2, for the white matter segmentation
                      _seg3, for the csf segmentation
                      or with the prefix (spm8)
                      c1, for the gray matter segmentation
                      c2, for the white matter segmentation
                      c3, for the csf segmentation
                    
    cfg.smooth      = 'no', or scalar, the FWHM of the gaussian kernel in
                        voxels, default depends on the requested output
    cfg.threshold   = 'no', or scalar, relative threshold value which is
                        used to threshold the data in order to create a
                        volumetric mask (see below).
                        the default depends on the requested output 
    cfg.downsample  = integer, amount of downsampling before segmentation
                        (default = 1; i.e., no downsampling)
    cfg.coordsys    = string, specifying the coordinate system in which the
                        anatomical data is defined. This will be used if
                        the input mri does not contain a coordsys-field.
                        (default = '', which results in the user being
                        forced to evaluate the coordinate system)
    cfg.units       = the physical units in which the output will be
                        expressed. (default = 'mm')
 
  Example use:
 
    segment = ft_volumesegment([], mri) will segment the anatomy and will output
                the segmentation result as 3 probabilistic masks in 
                segment.gray/.white/.csf
 
    cfg.output = 'skullstrip';
    segment    = ft_volumesegment(cfg, mri) will generate a skullstripped anatomy
                   based on a brainmask generated from the probabilistic
                   tissue maps. The skull-stripped anatomy is be stored in
                   the field segment.anatomy.
 
 
    cfg.output = {'brain' 'scalp' 'skull'};
    segment    = ft_volumesegment(cfg, mri) will produce a volume with 3 binary
                   masks, representing the brain surface, scalp surface, and skull
 
  For the SPM-based segmentation to work, the coordinate frame of the input
  MRI needs to be approximately coregistered to the templates of the
  probabilistic tissue maps. The templates are defined in SPM/MNI-space.
  FieldTrip attempts to do an automatic alignment based on the
  coordsys-field in the mri, and if this is not present, based on the
  coordsys-field in the cfg. If none of them is specified the
  FT_DETERMINE_COORDSYS function is used to interactively assess the
  coordinate system in which the MRI is expressed.
 
  The template mri is defined in SPM/MNI-coordinates:
    x-axis pointing to the right ear
    y-axis along the acpc-line
    z-axis pointing to the top of the head
    origin in the anterior commissure.
  Note that the segmentation only works if the template MRI is in SPM
  coordinates.
  
  If the input mri is a string pointing to a CTF *.mri file, the
  x-axis is assumed to point to the nose, and the origin is assumed
  to be on the interauricular line. In this specific case, when ft_read_mri
  is used to read in the mri, the coordsys field is automatically attached.
 
  To facilitate data-handling and distributed computing with the peer-to-peer
  module, this function has the following options:
    cfg.inputfile   =  ...
    cfg.outputfile  =  ...
  If you specify one of these (or both) the input data will be read from a *.mat
  file on disk and/or the output data will be written to a *.mat file. These mat
  files should contain only a single variable, corresponding with the
  input/output structure.
 
  See also FT_READ_MRI FT_DETERMINE_COORDSYS