External Email - Use Caution
Thanks again for your quick response. I ran trac-all -prep, and I am now
running bedpostx like you suggested. Will I need to create symlinks to tie
together the trac-preproc outputs and the inputs expected by bedpostx? If so,
would this be the appropriate linking:
ln -sf /dti_dir/dlabel/diff/lowb_brain_mask /dti_dir/dmri/nodif_brain_mask
Or should I be running bedpostx with a different mask?
Thanks again,
Amy
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@mgh.harvard.edu>
Sent: Wednesday, March 23, 2022 10:28 AM
To: Freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] bedpostx error inside trac-all
* External Email - Caution *
If you want to run it locally, then yes, running plain bedpostx should work.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mirro, Amy
<ami...@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
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia
<ayend...@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
* External Email - Caution *
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mirro, Amy
<ami...@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
External Email - Use Caution
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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