Cortical Hubs

The 'Cortical Hubs' (CHubs) are regions-of-interest defined by cortical thickness differences between older controls and individuals classified as having AD, created using the OASIS data set. These ROIS were used in the study The Dynamics of Cortical and Hippocampal Atrophy in Alzheimer Disease, Sabuncu et al.. See also: Supplemental and the snapshot of a figure from the paper below.

Freesurfer v5.2 (and v5.1 local) contains these ROIs as labels, found in the directory $FREESURFER_HOME/subjects/fsaverage/label. There are eight:

FS label name

name used in paper


inferior frontal cortex


inferior parietal cortex


inferior parietal sulcus


lateral temporal cortex


not used in paper


medial temporal lobe (eg. entorhinal cortex)


posterior cingulate


temporalpolar cortex

These labels are also combined into .annot files: ?h.oasis.chubs.annot

To view these on the fsaverage rh surface:

tksurfer fsaverage rh inflated -annotation oasis.chubs

To map these labels to your subject set (defined in SUBJECTS):

foreach s ($SUBJECTS)
    echo $s
    foreach h (lh rh)
        foreach l (oasis.chubs.ifc \
  .oasis.chubs.ipc \
  .oasis.chubs.ips \
  .oasis.chubs.lateraltemporal \
  .oasis.chubs.mtl \
  .oasis.chubs.retrosplenial \
            set cmd=(mri_label2label \
                --srclabel fsaverage/label/${h}${l} \
                --srcsubject fsaverage \
                --trgsubject $s \
                --trglabel $s/label/${h}${l} \
                --regmethod surface \
                --hemi $h)
            echo $cmd





These are a bunch of scripts (in the /scripts dir) which performed that mappings... see *chubs* files.