FT_DATATYPE_SEGMENTATION
Note that this reference documentation is identical to the help that is displayed in MATLAB when you type “help ft_datatype_segmentation”.
FT_DATATYPE_SEGMENTATION describes the FieldTrip MATLAB structure for segmented voxel-based data and atlasses. A segmentation can either be indexed or probabilistic (see below). A segmentation is a volumetric description which is usually derived from an anatomical MRI, which describes for each voxel the tissue type. It for example distinguishes between white matter, grey matter, csf, skull and skin. It is mainly used for masking in visualization, construction of volume conduction models and for construction of cortical sheets. An volume-based atlas is basically a very detailed segmentation with an anatomical label for each voxel. For example, the AFNI TTatlas+tlrc segmented brain atlas (which can be created with FT_READ_ATLAS) looks like this dim: [161 191 141] the size of the 3D volume in voxels transform: [4x4 double] affine transformation matrix for mapping the voxel coordinates to head coordinate system coordsys: 'tal' the transformation matrix maps the voxels into this (head) coordinate system unit: 'mm' the units in which the coordinate system is expressed brick0: [161x191x141 uint8] integer values from 1 to N, the value 0 means unknown brick1: [161x191x141 uint8] integer values from 1 to M, the value 0 means unknown brick0label: {Nx1 cell} brick1label: {Mx1 cell} An example segmentation with binary values that can be used for construction of a BEM volume conduction model of the head looks like this dim: [256 256 256] the dimensionality of the 3D volume transform: [4x4 double] affine transformation matrix for mapping the voxel coordinates to head coordinate system coordsys: 'ctf' the transformation matrix maps the voxels into this (head) coordinate system unit: 'mm' the units in which the coordinate system is expressed brain: [256x256x256 logical] binary map representing the voxels which belong to the brain scalp: [256x256x256 logical] binary map representing the voxels which belong to the scalp skull: [256x256x256 logical] binary map representing the voxels which belong to the skull An example of a whole-brain anatomical MRI that was segmented using FT_VOLUMESEGMENT looks like this dim: [256 256 256] the size of the 3D volume in voxels transform: [4x4 double] affine transformation matrix for mapping the voxel coordinates to head coordinate system coordsys: 'ctf' the transformation matrix maps the voxels into this (head) coordinate system unit: 'mm' the units in which the coordinate system is expressed gray: [256x256x256 double] probabilistic map of the gray matter white: [256x256x256 double] probabilistic map of the white matter csf: [256x256x256 double] probabilistic map of the cerebrospinal fluid The examples above demonstrate that a segmentation can be indexed, i.e. consisting of subsequent integer numbers (1, 2, ...) or probabilistic, consisting of real numbers ranging from 0 to 1 that represent probabilities between 0% and 100%. An extreme case is one where the probability is either 0 or 1, in which case the probability can be represented as a binary or logical array. The only difference to the volume data representation is that the segmentation structure contains the additional fields xxx and xxxlabel. See FT_DATATYPE_VOLUME for further details. Required fields: - dim, transform Optional fields: - coordsys, unit Deprecated fields: - none Obsoleted fields: - none Revision history: (2012/latest) The explicit distunction between the indexed and probabilistic representation was made. For the indexed representation the additional xxxlabel cell-array was introduced. (2005) The initial version was defined. See also FT_DATATYPE, FT_DATATYPE_VOLUME, FT_DATATYPE_PARCELLATION