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I simply put the desired brains in SUBJECTS_DIR, and then with SUBJECTS_DIR as the pwd, type quantifyThalamicSubnuclei.sh thal.txt T1

and that works. Perhaps drop mentioning the parent directories?

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of O'Dor, Sarah Louise SODOR@mgh.harvard.edu Sent: Tuesday, May 10, 2022 12:37 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [External] [Freesurfer] Compiling thalamic nuclei segmentation volumes

Good morning,

I apologize in advance that my background is not in coding. I have run the freesurfer thalamic segmentation tool on over 100 subjects. I am now trying to compile the data. I know that the instructions for this command are:

quantifyThalamicNuclei.sh <output_file> <analysisID> <OPTIONAL_SUBJECTS_DIR>

For <output_file>, I have specified the name and location for the text file it will generate.

For <analysisID>, I’m using the T1 that was processed through freesurfer, so I simply put T1.

For <OPTIONAL_SUBJECTS_DIR>, I specify the subject directory.

When I run the script above as:

quantifyThalamicNuclei.sh [complete path]/ThalamicSegSheet.txt T1 [complete path]/Subjects/

The response is:

Gathering results from subjects in:

[complete path]/Subjects

And writing them to:

[complete path]/ThalamicSegSheet.txt

…but nothing is generated. Any advice? I’d hate to compile the date individually for over 100 subjects.

Many thanks,

Sarah