[Freesurfer] -bash: segmentThalamicNuclei.sh: command not found

[Parisi Veronica]

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.


After the download of the dev version, I followed the 
http://freesurfer.net/fswiki/ThalamicNuclei?action=fullsearch=180=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=get=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




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[Freesurfer] thalamic segmentation analysis

[Parisi Veronica]

External Email - Use Caution

Hi there,

I have been trying to learn and set-up Freesurfer for a research project I am 
working on, but I am having trouble with the set-up/installation process.

Once Freesurfer is set-up, I will be using it to measure thalami and define 
their sub nuclei.

I have followed the instructions online to the best of my ability but can't 
seem to figure this out. Any assistance would be very much appreciated.

Thank you.

Best,


VP


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Respect the environment: print this email only if necessary.
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