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Hello FreeSurfers,

I have a student who is trying to run the segmentThalamicNuclei module on some T1 images, using the segmentThalamicNuclei.sh script.

All of the subjects have been run through the main recon-all pipeline and each participant has their own folder in the directory which is set to SUBJECTS_DIR containing this output. When calling segmentThalamicNuclei.sh with a subject ID, nothing happens except the following is printed in the terminal:

If: Expression syntax.

We are assuming that the SUBJECT_ID here corresponds to the name of a participant folder inside of SUBJECTS_DIR containing their recon-all output - is this correct? Is this a syntax error inside of segmentThalamicNuclei.sh, or is there an issue in the way that we are trying to run it?

The student is using MacOS Ventura V13.4.1, FreeSurfer V7.4.1, and has the v2019b MATLAB runtime installed.

Thank you for any advice!

Best wishes, Rowan

__________________________________________________________________________________________________ GTA/PhD Candidate School of Health Sciences Zochonis G30, M13 9NT