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reference:ft_datatype_segmentation [2018/08/23 14:43] (current)
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 +=====  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"​.
 +
 +<​html><​pre>​
 +  <a href=/​reference/​ft_datatype_segmentation><​font color=green>​FT_DATATYPE_SEGMENTATION</​font></​a>​ 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 <a href=/​reference/​ft_read_atlas><​font color=green>​FT_READ_ATLAS</​font></​a>​) 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 <a href=/​reference/​ft_volumesegment><​font color=green>​FT_VOLUMESEGMENT</​font></​a>​
 +  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 <a href=/​reference/​ft_datatype_volume><​font color=green>​FT_DATATYPE_VOLUME</​font></​a>​ 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 <a href=/​reference/​ft_datatype><​font color=green>​FT_DATATYPE</​font></​a>,​ <a href=/​reference/​ft_datatype_volume><​font color=green>​FT_DATATYPE_VOLUME</​font></​a>,​ <a href=/​reference/​ft_datatype_parcellation><​font color=green>​FT_DATATYPE_PARCELLATION</​font></​a>​
 +</​pre></​html>​