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-boun...@nmr.mgh.harvard.edu> on behalf of Parisi Veronica <parisi.veron...@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 External Email - Use Caution 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.dmg<https://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=180&value=linkto%3A%22ThalamicNuclei%22 instruction as reported: - export FREESURFER_HOME=/Users/vp/freesurfer - cd $FREESURFER_HOME - curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bMAC.tar.gz"; -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 Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary.
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