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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Hi

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?

Thanks

Regards

Amrita