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/FreeSurferColorLUT) 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.han...@regionh.dk / morten.sejer.han...@dadlnet.dk<mailto:morten.sejer.han...@regionh.dk%20/%20morten.sejer.han...@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.dk<http://www.regionh.dk/> This e-mail and any attachment may contain confidential and privileged material intended for the addressee only. If you are not the addressee, you are notified that no part of the e-mail or any attachment may be disclosed, copied or distributed, and that any other action related to this e-mail or attachment is strictly prohibited, and may be unlawful. If you have received this e-mail by error, please notify the sender immediately by return e-mail, and delete this message. ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.
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