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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.

attachment:annot-sm.jpg

Background

• [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Automatically Parcellating the Human Cerebral Cortex], Fischl et al., (2004). Cerebral Cortex, 14:11-22.

• [https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest], Desikan et al., (2006). NeuroImage, in press.

Utilities

• ["mris_sample_parc"] - samples a volumetric parcellation onto a surface
• ["mris_ca_train"] - creates the reference atlas
• ["mris_ca_label"] - parcellates a cortical surface based on the reference atlas

Atlases

• There are two atlases included with Freesurfer:

  • $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs - see [https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf Desikan et al., (2006)].

  • $FREESURFER_HOME/average/?h.atlas2005_simple.gcs - see [https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf Fischl et al., (2004)].

• To create your own atlas, see the example in ["mris_ca_train"].

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

Cingulate (if you want to include in a lobe)

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