Hi Veronica Did you source FreeSurfer? After that, the command would be: segmentThalamicNuclei.sh A7 /Users/vp/freesurfer/ANALISI_DATA/ Cheers, /Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Parisi Veronica parisi.veronica@hsr.it Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, April 17, 2020 at 20:08 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] -bash: segmentThalamicNuclei.sh: command not found

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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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