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