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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 [[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]] | 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 [[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 the snapshot of a figure from the paper below. |
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|| ?h.oasis.chubs.medialpfc || not used in paper || | || ?h.oasis.chubs.medialpfc || '''not used in paper''' || |
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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 $s foreach h (lh rh) foreach l (oasis.chubs.ifc \ .oasis.chubs.ipc \ .oasis.chubs.ips \ .oasis.chubs.lateraltemporal \ .oasis.chubs.mtl \ .oasis.chubs.retrosplenial \ .oasis.chubs.tp) set cmd=(mri_label2label \ --srclabel fsaverage/label/${h}${l} \ --srcsubject fsaverage \ --trgsubject $s \ --trglabel $s/label/${h}${l} \ --regmethod surface \ --hemi $h) echo $cmd $cmd end end end }}} |
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=== Notes: === * While the paper says these are from the [[OASIS]] data set, they are actually from an earlier data set created at Washington University which later was 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 that mappings... see *chubs* files. |
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 $FREESURFER_HOME/subjects/fsaverage/label. There are eight:
FS label name |
name used in paper |
?h.oasis.chubs.ifc |
inferior frontal cortex |
?h.oasis.chubs.ipc |
inferior parietal cortex |
?h.oasis.chubs.ips |
inferior parietal sulcus |
?h.oasis.chubs.lateraltemporal |
lateral temporal cortex |
?h.oasis.chubs.medialpfc |
not used in paper |
?h.oasis.chubs.mtl |
medial temporal lobe (eg. entorhinal cortex) |
?h.oasis.chubs.retrosplenial |
posterior cingulate |
?h.oasis.chubs.tp |
temporalpolar cortex |
These labels are also combined into .annot files: ?h.oasis.chubs.annot
To view these on the fsaverage rh surface:
tksurfer fsaverage rh inflated -annotation oasis.chubs
To map these labels to your subject set (defined in SUBJECTS):
foreach s ($SUBJECTS) echo $s foreach h (lh rh) foreach l (oasis.chubs.ifc \ .oasis.chubs.ipc \ .oasis.chubs.ips \ .oasis.chubs.lateraltemporal \ .oasis.chubs.mtl \ .oasis.chubs.retrosplenial \ .oasis.chubs.tp) set cmd=(mri_label2label \ --srclabel fsaverage/label/${h}${l} \ --srcsubject fsaverage \ --trgsubject $s \ --trglabel $s/label/${h}${l} \ --regmethod surface \ --hemi $h) echo $cmd $cmd end end end
Notes:
While the paper says these are from the OASIS data set, they are actually from an earlier data set created at Washington University which later was 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 that mappings... see *chubs* files.