Hi Amy - This will have the same effect as running it locally. All the the *_mgh version does is submit each slice as a separate job on a certain type of cluster. If you run trac-all with --jobs <filename> , it will save a text file with the commands that would've been submitted as jobs, instead of actually trying to submit them. Then you can submit them to a cluster yourself, using the syntax that's specific to your cluster.

Anastasia.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mirro, Amy <amirro@wustl.edu>
Sent: Wednesday, March 23, 2022 10:04 AM
To: Freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] bedpostx error inside trac-all
 

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Hello, 

I am trying to run trac-all -bedp and I am running into the following error: 

/opt/freesurfer/bin/bedpostx_mgh: 128: /opt/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected


Others have encountered this error previously, and you had advised running bedpostx locally (as oppsoed to bedpostx_mgh). I was wondering, however, if there is a way to still run bedpostx inside trac-all. 

I was looking at the source code for trac-all in your github (branch 7.2), and I noticed that line 611 calls bedpostx_mgh despite being within the "if (! $onpbs)" conditional. Would changing line 611 from: 

          set cmd = (bedpostx_mgh -n $nstick -model 1 $dtdir/dmri)
to 
          set cmd = (bedpostx -n $nstick -model 1 $dtdir/dmri)

fix the problem? 

If it's helpful:
I am running on centos7 and my build stamp is: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Thanks, 
Amy

 

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