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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.

Background

Automatically Parcellating the Human Cerebral Cortex, Fischl et al., (2004). Cerebral Cortex, 14:11-22.
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 (produces .gcs 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).
- $FREESURFER_HOME/average/?h.atlas2005_simple.gcs - see Fischl et al., (2004).
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)

-Deletions are marked like this.
+Additions are marked like this.
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-[wiki:Self:FreeSurferWiki top]
+[[FreeSurferWiki|top]]
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-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.
+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.
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-attachment:annot-sm.jpg
+{{attachment:annot-sm.jpg}}
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- * [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/fischl04-parcellation.pdf|Automatically Parcellating the Human Cerebral Cortex]], Fischl et al., (2004). Cerebral Cortex, 14:11-22.
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- * [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.
+ * [[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.
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- * ["mris_sample_parc"] - samples a volumetric parcellation onto a surface
+ * [[mris_sample_parc]] - samples a volumetric parcellation onto a surface
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- * ["mris_ca_train"] - creates the reference atlas (produces .gcs files)
+ * [[mris_ca_train]] - creates the reference atlas (produces .gcs files)
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- * ["mris_ca_label"] - parcellates a cortical surface based on the reference atlas (produces .annot files)
+ * [[mris_ca_label]] - parcellates a cortical surface based on the reference atlas (produces .annot files)
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-  * $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"].  See also: SurfaceRegAndTemplates and ["tksurfer_labeledit"].
+  * $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]].  See also: SurfaceRegAndTemplates and [[tksurfer_labeledit]].
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-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:
+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: