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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)

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	== 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)