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)

Destrieux Atlas (?h.aparc.a2009s.annot)

DKT Atlas (?h.aparc.DKTatlas40.annot)








.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 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 'Desikan-Killiany' ROIs (found in ?h.aparc.annot) to the lobes:





Cingulate (if you want to include in a lobe)

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.

CorticalParcellation (last edited 2014-11-11 21:49:16 by NickSchmansky)