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Dear Freesurfer Support Team,

I'm trying to run the segmentThalamicNuclei.sh to segment the thalamic nuclei on a subject. I am using the latest Freesurfer dev version (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/). I previously ran recon-all to generate the required files for the thalamic segmentation tool using the version freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmghttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg.

After the download of the dev version, I followed the http://freesurfer.net/fswiki/ThalamicNuclei?action=fullsearch&context=18... instruction as reported:

- export FREESURFER_HOME=/Users/vp/freesurfer

- cd $FREESURFER_HOME

- curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&am..." -o "runtime.tar.gz"

- tar xvf runtime.tar.gz

- rm $FREESURFER_HOME/runtime.tar.gz

- segmentThalamicNuclei.sh bert [SUBJECTS_DIR] =

segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/A7/mri/norm.mgz

However, the program exits with the following error message:

-bash: segmentThalamicNuclei.sh: command not found

It doesn't seem to me that there are errors in the paths.

What can I do to fix the problem?

Thank you, VP

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