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    * Subject output is named <subjid>/label/?h.aparc.annot
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    * Subject output is named <subjid>/label/?h.aparc.a2005s.annot

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Cortical Parcellation

The FreeSurfer utilities mris_ca_train and mris_ca_label together implement a technique for automatically assigning a neuroanatomical label to each location on a cortical surface model based on probabilistic information estimated from a manually labeled training set (made using FreeSurfer). This procedure incorporates both geometric information derived from the cortical model, and neuroanatomical convention, as found in the training set. The result is a complete labeling of cortical sulci and gyri.

Desikan-Killiany Atlas

Destrieux Atlas

annot-desikan.jpg

annot-destrieux.jpg

Background

Utilities

  • mris_sample_parc - samples a volumetric parcellation onto a surface

  • mris_label2annot - creates a .annot file from a set of labels and a colortable, for input to mris_ca_train

  • mris_ca_train - creates the reference atlas (produces .gcs files from a set of .annot files)

  • mris_ca_label - parcellates a cortical surface based on the reference atlas (produces .annot files)

Atlases

  • There are two atlases included with Freesurfer (created in-house using mris_ca_train):
    • $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs - see Desikan et al., (2006).

      • This atlas is also known as the 'Desikan-Killiany' cortical atlas. It is a gyral based atlas: ie, a gyrus was defined as running between the bottoms of 2 adjacent sulci. That is, a gyrus includes the part visible on the pial view + adjacent banks of the sulci limiting this gyrus.
      • Subject output is named <subjid>/label/?h.aparc.annot

    • $FREESURFER_HOME/average/?h.atlas2005_simple.gcs - see Fischl et al., (2004).

      • This atlas is also known as the 'Destrieux' cortical atlas. It is based on parcellation that first divided the cortex in gyral and sulcal, the limit between both being given by the curvature value of the surface. A gyrus only includes the cortex visible on the pial view, the hidden cortex (banks of sulci) are marked sulcus.
      • Subject output is named <subjid>/label/?h.aparc.a2005s.annot

  • To create your own atlas, see the example in mris_ca_train. See also: SurfaceRegAndTemplates and tksurfer_labeledit.

.annot files

After Freesurfer processes a subject, in the subject's /label directory, there are .annot files containing the parcellation data for each hemishere. The ?h.aparc.annot files contain the desikan_killiany.gcs parcellation scheme, while the ?h.aparc.a2005s.annot files contain the atlas2005_simple.gcs scheme. The data in the .annot files can be read using the matlab script read_annotation.m (also found in $FREESURFER_HOME/matlab). Example usage:

>> [vertices,label,colortable]=read_annotation('rh.aparc.annot');

Where vertices is just each vertex number. label contains the parcellation label for that vertex, where the label is a colortable number. For instance, if a label is '6553700', then find that number in the colortable.table structure, and its label name is that same index in the colortable.struct_name structure (in this example, '6553700' is 'frontalpole').

Lobe mapping

While some ROIs cross two or more lobar boundaries (i.e. fusiform), others (i.e. cingulate subdivisions) can be considered separately or can be included to follow the 4 lobes. The following is an approximate mapping of individual ROIs (found in ?h.aparc.annot) to the lobes:

Frontal

  • Superior Frontal
  • Rostral and Caudal Middle Frontal
  • Pars Opercularis, Pars Triangularis, and Pars Orbitalis
  • Lateral and Medial Orbitofrontal
  • Precentral
  • Paracentral
  • Frontal Pole

Parietal

  • Superior Parietal
  • Inferior Parietal
  • Supramarginal
  • Postcentral
  • Precuneus

Temporal

  • Superior, Middle, and Inferior Temporal
  • Fusiform
  • Transverse Temporal
  • Entorhinal
  • Temporal Pole
  • Parahippocampal

Occipital

  • Lateral Occipital
  • Lingual
  • Cuneus
  • Pericalcarine

Cingulate (if you want to include in a lobe)

  • Rostral Anterior (Frontal)
  • Caudal Anterior (Frontal)
  • Posterior (Parietal)
  • Isthmus (Parietal)

CorticalParcellation (last edited 2021-04-29 10:56:24 by DevaniCordero)