Dear Experts,
I am interested in retrieving the volume of the insula and substantia nigra from T1W structural scans converted to nii.gz files. All scans have undergone the recon-all process without error. I have seen volume estimations of Insula and substantia nigra performed in several studies, but I can't seem to figure out how I retrieve these volumes.
I ran the command:
asegstats2table --subjects 1_T1W_recon-all 2_T1W_recon-all 3_T1W_recon-all 4_T1W_recon-all 5_T1W_recon-all --meas volume --tablefile Subcortical.txt
SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Building the table.. Writing the table to Subcortical.txt
following this I get at fine output with several volume estimation of subcortical structures, but without the Insula (left and right), and without the substantia nigra (left and right).
I tried to run the same command on "Bert", and ended up with the same result (with the insula and substania nigra still missing). I also tried to add the
--all-segs
But without any change in the output.
On the FreeSurferColorLUT (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfe...) I can see that the structures I am interested in have the following numbers: 19, 27, 55 and 59.
Could you provide me answers on how to extract the volumes of the insula and substantia nigra?
Thanks a lot!
Kind regards
Morten Sejer Hansen
Morten Sejer Hansen MD Direct: + 45 26373611 Mail: morten.sejer.hansen@regionh.dk / morten.sejer.hansen@dadlnet.dkmailto:morten.sejer.hansen@regionh.dk%20/%20morten.sejer.hansen@dadlnet.dk
Department of anaesthesiology 4231 Centre of head and orthopaedics Copenhagen University Hospital, Rigshospitalet Blegdamsvej 9 2100 Copenhagen
Tel: +45 35 45 35 45 Web: www.regionh.dkhttp://www.regionh.dk/
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