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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 (?h.aparc.annot)''' ||<style="text-align:center" |2>'''Destrieux Atlas (?h.aparc.a2009s.annot)''' ||
||'''DKT Atlas''' '''(?h.aparc.DKTatlas40.annot''') ||
|| {{attachment:annot-desikan.jpg}} || {{attachment:annot-destrieux.jpg}} ||
|| {{attachment:annot-desikan-m.jpg}} || {{attachment:annot-destrieux-m.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, 31(3):968-80.
 * [[http://mindboggle.info/data.html|DKT40 classifier atlas: FreeSurfer atlas (.gcs) from 40 of the Mindboggle-101 participants (2012)]]

== 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 three atlases included with Freesurfer:
  * $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs - see [[https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf|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 two 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.destrieux.simple.2009-07-29.gcs - see [[https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf|Fischl et al., (2004)]] and [[https://www.sciencedirect.com/science/article/pii/S1053811910008542| Destrieux et al. (2010)]].
   * This atlas is also known as the 'Destrieux' cortical atlas. It is based on a parcellation scheme that first divided the cortex into gyral and sulcal regions, 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.a2009s.annot
   * Atlas changed August 2009.  See DestrieuxAtlasChanges.
  * $FREESURFER_HOME/average/?h.DKTatlas40.gcs
   * [[http://mindboggle.info/data.html|DKT40 classifier atlas]]
   * [[attachment:README-DKT40.txt|40 of the 101 mindboggle subjects were used]]
   * [[http://media.mindboggle.info/data/atlases/classifiers/make_freesurfer_classifier_atlas.txt|script used to build]]
 * 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.

 * ?h.aparc.annot files contain the desikan_killiany.gcs parcellation scheme
 * ?h.aparc.a2009s.annot files contain the destrieux.simple.2009-07-28.gcs scheme
 * ?h.aparc.DKTatlas.annot correspond to the DKTatas40.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 'Desikan-Killiany' ROIs (found in ?h.aparc.annot) to the lobes, [[https://www.frontiersin.org/articles/10.3389/fnins.2012.00171/full#h12|described in the Appendix of this publication]]:

=== 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
 * Banks of the Superior Temporal Sulcus
 * 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)

You can use [[mri_annotation2label]] to extract the individual labels of an existing cortical parcellation and then mri_mergelabels to fuse those labels together to form a lobe.

{{{
mri_annotation2label  --subject subjid --hemi rh --outdir ./location
mri_mergelabels -i label1 -i label2 -o outputlabel
}}}
For FS V5.0 and later, you can also run mri_annotation2label with --lobesStrict to get a lobe annotation. If that definition of "lobes" is good for you, then you can run mris_anatomical_stats to get the volume for each lobe.

For earlier versions, you can use  mri_annotation2label to break the labels apart, then use mri_mergelabels to combine the individual labels into lobe labels, then use mris_label2annot to create a lobe annotation, then use mris_anatomical_stats.

mri_annotation2label --help will show you more options that are available to you.