Dear Amrita, Please insert your subject directory between your subject name(sub-19253779) and your FGATIR scan (sub-19253779/mri/FGATIR.nii.gz). If you running your code from the subjects directory, which seems to be the case, it would simply be: segmentThalamicNuclei.sh sub-19253779 . sub-19253779/mri/FGATIR.nii.gz FGATIR t2 Cheers, /E

-- Juan Eugenio Iglesias http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Pal, Amrita Amrita.Pal@corewellhealth.org Date: Wednesday, November 22, 2023 at 10:25 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unable to add FGATIR during thalamic segmentation

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I am unable to add an additional scan FGATIR during thalamic segmentation. For example I have a subject in the freesurfer/subjects directory that does thalamic segmentation without adding the additional scan but not with the attached code. I tried different flags but that didn’t work. Can you please help? [cid:image001.png@01DA1D2E.1672BBD0] Thanks Regards Amrita