= 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 [[JenniNotes/Oasis|OASIS]] data set.  These ROIs were used in the study [[https://surfer.nmr.mgh.harvard.edu/pub/articles/Sabuncu2011_Archives_InPress.pdf|The Dynamics of Cortical and Hippocampal Atrophy in Alzheimer Disease, Sabuncu et al.]].  See also: [[https://surfer.nmr.mgh.harvard.edu/pub/articles/Sabuncu_ArchivesOfNeurology_2011_Supplemental.pdf|Supplemental]], and below is a snapshot of a figure from the paper.

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''' ||
|| ?h.oasis.chubs.ifc || inferior frontal cortex ||
|| ?h.oasis.chubs.ipc || inferior parietal cortex ||
|| ?h.oasis.chubs.ips || inferior parietal sulcus ||
|| ?h.oasis.chubs.lateraltemporal || lateral temporal cortex ||
|| ?h.oasis.chubs.medialpfc || '''not used in paper''' ||
|| ?h.oasis.chubs.mtl || entorhinal cortex (medial temporal lobe) ||
|| ?h.oasis.chubs.retrosplenial || posterior cingulate ||
|| ?h.oasis.chubs.tp || 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 (which you would define in a SUBJECTS csh shell var), first you will need to symlink the fsaverage subject into your own subjects dir:
{{{
cd $SUBJECTS_DIR
ln -s $FREESURFER_HOME/subjects/fsaverage
}}}
Confirm that you see 16 .label files and two .annot files:
{{{
ls $SUBJECTS_DIR/fsaverage/label/*chubs*
}}}

Now you can do the mapping:

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

You will probably want to have these labels combined into a .annot file so that mris_anatomical_stats can operate on this set of labels, so to create this .annot file, first you will need a colortable.  Create this text file, naming it {{{colortable_oasis_chubs.txt}}}, and put it in your {{{$SUBJECTS_DIR/scripts}}} dir:
{{{
  0  unknown                        25   5  25   0
  1  oasis.chubs.ifc                25 100  40   0
  2  oasis.chubs.ipc               125 100 160   0
  3  oasis.chubs.ips               220  60 220   0
  4  oasis.chubs.lateraltemporal   120  70  50   0
  5  oasis.chubs.medialpfc         220  20 100   0
  6  oasis.chubs.mtl               220  20  10   0
  7  oasis.chubs.retrosplenial     140  20 140   0
  8  oasis.chubs.tp                200  35  75   0
}}}

Now you can run this script to create the file {{{?h.oasis.chubs.annot}}} in the {{{/label}}} directory of each of your subjects:
{{{
foreach subj ($SUBJECTS)
  foreach hemi (lh rh)
    cd $SUBJECTS_DIR/$s/label
    set cmd=(mris_label2annot \
      --s $subj \
      --hemi $hemi \
      --ctab $SUBJECTS_DIR/scripts/colortable_oasis_chubs.txt \
      --l $hemi.oasis.chubs.ifc.label \
      --l $hemi.oasis.chubs.ipc.label \
      --l $hemi.oasis.chubs.ips.label \
      --l $hemi.oasis.chubs.lateraltemporal.label \
      --l $hemi.oasis.chubs.medialpfc.label \
      --l $hemi.oasis.chubs.mtl.label \
      --l $hemi.oasis.chubs.retrosplenial.label \
      --l $hemi.oasis.chubs.tp.label \
      --a oasis.chubs)
    echo $cmd
    $cmd
  end
end
cd $SUBJECTS_DIR
}}}

Last but not least, a snaphot from the Sabuncu paper:
{{attachment:chubs.jpg}}

=== Notes: ===
 * While the paper says these are from the [[JenniNotes/Oasis|OASIS]] data set, they are actually from an earlier data set created at Washington University whose subjects were later included in the OASIS data set.  The data set used to create these CHubs is found in the NMR Center here:

{{{
/autofs/cluster/con_008/users/washu
}}}

 * The CHubs ROIs were mapped to the ADNI data set.  The ADNI data set is found here:

{{{
/autofs/cluster/con_009/users/ADNI
}}}

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