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: rb3419@cumc.columbia.edu mailto:rb3419@cumc.columbia.edu _https://indiaalliance.org/fellow/rakshathi-basavaraju_

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