Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the .csh file which has all the TRACULA configuration info, and also to the bash script that I’m running the trac-all from: export ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Nasiriavanaki, Zahra,M.D. <ZNASIRIAVANAKI@mgh.harvard.edu>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Tracula error
 
Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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