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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
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