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 * To create your own atlas, see the example in ["mris_ca_train"]. See also: SurfaceRegAndTemplates  * To create your own atlas, see the example in ["mris_ca_train"]. See also: SurfaceRegAndTemplates and ["tksurfer_labeledit"].

[wiki:FreeSurferWiki top]

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.

attachment:annot-sm.jpg

Background

Utilities

  • ["mris_sample_parc"] - samples a volumetric parcellation onto a surface
  • ["mris_ca_train"] - creates the reference atlas (produces .gcs files)
  • ["mris_ca_label"] - parcellates a cortical surface based on the reference atlas (produces .annot files)

Atlases

.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 attachment: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)