FT_VOLUMESEGMENT

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
    segmented = ft_volumesegment(cfg, mri)
  where the input mri should be a single anatomical volume that was for example read with
  FT_READ_MRI. For the purpose of creating binary masks of the brain or of the skull, you can also
  provide either the anatomical volume or the already segmented volume (with the probabilistic
  tissue maps) as input.
 
  The configuration structure can contain
    cfg.output         = string or cell-array of strings, see below (default = 'tpm')
    cfg.spmversion     = string, 'spm2' or 'spm8' (default = 'spm8')
    cfg.template       = filename of the template anatomical MRI (default = '/spm2/templates/T1.mnc'
                         or '/spm8/templates/T1.nii')
    cfg.tpm            = cell-array containing the filenames of the tissue probability maps
    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.brainsmooth    = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)
    cfg.scalpsmooth    = 'no', or scalar, the FWHM of the gaussian kernel in voxels, (default = 5)
    cfg.brainthreshold = 'no', or scalar, relative threshold value which is used to threshold the
                        tpm in order to create a volumetric brainmask (see below), (default = 0.5)
    cfg.scalpthreshold = 'no', or scalar, relative threshold value which is used to threshold the
                         anatomical data in order to create a volumetric scalpmask (see below),
                         (default = 0.1)
    cfg.downsample     = integer, amount of downsampling before segmentation
                        (default = 1; i.e., no downsampling)
 
  The desired segmentation output is specified with cfg.output as a string or cell-array of strings
  and can contain
    'tpm'         - tissue probability map for csf, white and gray matter
    'brain'       - binary representation of the brain (including csf, white and gray matter)
    'skull'       - binary representation of the skull
    'scalp'       - binary representation of the scalp
    'skullstrip'  - anatomy with only the brain
 
 
  Example use:
    cfg        = [];
    segmented  = ft_volumesegment(cfg, mri) will segmented the anatomy and will output the
                 segmentation result as 3 probabilistic masks in segmented.gray, white and csf.
 
    cfg.output = 'skullstrip';
    segmented  = ft_volumesegment(cfg, mri) will generate a skull-stripped anatomy based on a
                 brainmask generated from the probabilistic tissue maps. The skull-stripped anatomy
                 is stored in the field segmented.anatomy.
 
    cfg.output = {'brain' 'scalp' 'skull'};
    segmented  = ft_volumesegment(cfg, mri) will produce a volume with 3 binary masks, representing
                 the brain surface, scalp surface, and skull which do not overlap.
 
    cfg.output = {'scalp'};
    segmented  = ft_volumesegment(cfg, mri) will produce a volume with a binary mask (based on the
                 anatomy), representing the border of the scalp surface (i.e., everything inside the
                 surface is also included). Such representation of the scalp is produced faster,
                 because it doesn't require to create the tissue probabilty maps before creating
                 the mask.
 
  It is not possible to request tissue-probability map (tpm)  in combination with binary masks
  (brain, scalp or skull) or skull-stripped anatomy. The output will return only the probabilistic
  maps in segmented.gray, white and csf. However, when a segmentation with the probabilistic gray, white
  and csf representations is available, it is possible to use it as input for brain or skull binary mask.
  For example:
    cfg           = [];
    cfg.output    = {'tpm'};
    segment_tpm   = ft_volumesegment(cfg, mri);
    cfg.output    = {'brain'};
    segment_brain = ft_volumesegment(cfg, segment_tpm);
 
  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 you can use
    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, FT_PREPARE_HEADMODEL

reference/ft_volumesegment.txt · Last modified: 2016/08/17 23:02 (external edit)

You are here: startreferenceft_volumesegment
CC Attribution-Share Alike 3.0 Unported
www.chimeric.de Valid CSS Driven by DokuWiki do yourself a favour and use a real browser - get firefox!! Recent changes RSS feed Valid XHTML 1.0
This DokuWiki features an Anymorphic Webdesign theme, customised by Eelke Spaak and Stephen Whitmarsh.
Mobile Analytics Website Security Test