If you want to run it locally, then yes, running plain bedpostx should work. ________________________________ 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 11:17 AM To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bedpostx error inside trac-all
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Thanks so much for the quick response!
Mimicking the behavior of a local run was my goal. Right now, I run all three "portions" of trac-all in one script (using the python code shown below):
# call each step in tracula trac_all_prep_call = ["trac-all", "-prep", "-c", f"{config_file}", "-log", f"{prep_log_file}"] trac_all_bed_call = ["trac-all", "-bedp", "-c", f"{config_file}", "-log", f"{bed_log_file}"] trac_all_path_call = ["trac-all", "-path", "-c" , f"{config_file}", "-log", f"{path_log_file}"] for trac_call in [trac_all_prep_call, trac_all_bed_call, trac_all_path_call]: o= subprocess.run(trac_call)
So my goal when suggesting that change was to have the trac-all -bedp command work when the onpbs variable is False. However, it sounds like you are saying that in order to run bedpost not on a cluster I need to do so "outside" of trac-all. So, should I replace the trac_all_bed_call above with something like:
bedpost -n $nstick -model 1 /path/to/subjects/dmri/directory
Would that work? Sorry if I am misunderstanding. Thanks so much for your help!
Thanks, Amy
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Sent: Wednesday, March 23, 2022 9:10 AM To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bedpostx error inside trac-all
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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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