On 10/26/2020 3:58 PM, Basavaraju, Rakshathi wrote:
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Dear Freesurfer team,
I have been trying to extract local gyrification index in a dataset
according to a label which I have created.
1) First of all, I extracted lGI as per DKT areas, which one is lGI
value in the ?h.pial_lgi.stats file (derived on running a lGI recon?)
# ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd
MeanCurv GausCurv FoldInd CurvInd
caudalanteriorcingulate 1094 774 2285 3.234
0.889 0.129 0.031 15 1.3
Is the lGI of caudal anterior cingulate 3.234 or 1.3?
It is 3.234
2) I could register a label which I have created to the surface of
individual subjects using mrilabel2label which ran alright, and I
could view the label on the surface of the individual subject intact
on freeview. But after that I am unable to extract lGI value from the
designated label only using mris_anatomicalstats.
I used the following command: mris_anatomical_stats -l
label/outlabelbase-0001.label -f stats/occipital_lGI.stats
FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh pial_lgi
This throws the error: #MRISread: file
'/mnt/share/projects/provenzano/Human/CHR_Rakshathi/LGI/FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE/surf/rh.pial_lgi'
has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
Try using mri_segstsats, like
mri_segstats --slabel subject rh label/outlabelbase-0001.label --id 1
--o mean.dat
Then I converted rh_pial.lgi to rh_pial.lgi.asc: mris_convert -c
rh.pial_lgi rh.white rh.pial_lgi.asc
and then ran: mris_anatomical_stats -l label/outlabelbase-0001.label
-f stats/occipital_lGI.stats FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh
pial_lgi.asc
then the error: Segmentation fault (core dumped)
Kindly help me, this analysis is way overdue, and it is seeming like
an endless tunnel only of new errors....
Dr. Rakshathi Basavaraju (MD Psychiatry)
Postdoctoral Research Scientist
Taub Institute for Research on Alzheimer's Disease and the Aging Brain
Columbia University Medical Centre
622 West, 168th Street, New York - 10032
E-Mail: rb3...@cumc.columbia.edu <mailto:rb3...@cumc.columbia.edu>
_https://indiaalliance.org/fellow/rakshathi-basavaraju_
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