Hi Ela,
It looks to me like line 79 of bedpostx_preproc.sh is:
if [ ${gflag} -eq 1 ]; then
Which is consistent with the error:
-eq: unary operator expected
What this error is saying is that the variable `gflag` has not been set, so the script does not know how to perform the comparison.
`gflag` is set a few lines above to the second parameter passed when executing `bedpostx_preproc.sh`. I would investigate how `bedpostx_preproc.sh` is being invoked to chase down the cause of this error.
-Paul ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Wednesday, June 8, 2022 12:32 PM To: Yendiki, Anastasia AYENDIKI@mgh.harvard.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA -bedp parallel processing
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That actually helps but not solving all the problems. So, what happens is that if I create dmri.bedpostX folder, the first error goes away, a.k.a. (cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a directory). However, the second error still exists: a.k.a. (home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator expected". line 79 is "${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask). And when I try to run Parallel lines, I still get the error (dmri.bedpostX/logs/log0000: No such file or directory). So, my guess is, it still doesn't copy the whole needed package for some reason. So, what we end up having in dmri.bedpostX folder is a)bvals, b)bvecs, c) nodif_brain_mask.nii.gz.
I can always manually copy all needed file from fsl folder to our subjects folder, but I am curious why we get the error and why everything is not copied automatically. I also don't know what files we need to manually copy.
Thanks again, Ela ________________________________ From: Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Sent: Tuesday, June 7, 2022 2:46 PM To: Salar Dini, Elaheh elaheh.salardini@yale.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: TRACULA -bedp parallel processing
What if you create the directory (that shows up in the "not a directory" error)? ________________________________ From: Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Tuesday, June 7, 2022 11:46 AM To: Yendiki, Anastasia AYENDIKI@mgh.harvard.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: TRACULA -bedp parallel processing
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Hi Anastasia,
FSL version is 6.0.5.1
Thanks,
Ela
To: Salar Dini, Elaheh elaheh.salardini@yale.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: Re: TRACULA -bedp parallel processin
Hi Ela - Which version of FSL are you using?
Anastasia.
________________________________ From: Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Monday, June 6, 2022 5:26 PM To: Yendiki, Anastasia AYENDIKI@mgh.harvard.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: TRACULA -bedp parallel processing
Thanks for the reply. I'm not sure if you are looking for this: we use a small cluster with 40 nodes, 512 CPU cores. We are still using PBS.
Thanks, Ela ________________________________ From: Yendiki, Anastasia AYENDIKI@mgh.harvard.edu Sent: Saturday, June 4, 2022 1:05 AM To: Salar Dini, Elaheh elaheh.salardini@yale.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: TRACULA -bedp parallel processing
What kind of cluster are you running the parallel processes on?
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Friday, June 3, 2022 7:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA -bedp parallel processing
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Thank you for the guidance.
When it tries to run pre.ParallelI , I'll get this:
Copying files to bedpost directory
cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is not a directory /home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator expected Done
This happens for all subjects.
After this, when I check the subject 57 folder in subjects_dir, there is a file named "dmri.bedpostX.nii.gz".
However, when it tries to run Parallel lines, these errors coming up:
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0000: No such file or directory /home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: /home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No such file or directory
...
If I run trac-all -bedp -c <Cinfig File> , and not try to process parallelly, it runs without any errors to the end.
Do you have any thoughts what goes wrong?
Thanks again,
Ela
You run them in that order. First the pre, then the parallel, then the post. You can queue them that way, so that the parallel jobs wait for the pre to finish, and the post waits for all the parallel jobs to finish.
________________________________ From: Salar Dini, Elaheh Sent: Friday, June 3, 2022 3:09 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: TRACULA -bedp parallel processing
Hello,
I have tried to create a text file with command lines that can be run in parallel by using trac-all -bedp -c <config file> -jobs Parallel. When I use this command three text files are produced named: pre.Parallel, post.Parallel, and Parallel. Should I just use Parallel as a source for command lines? What are pre.Parallel and post.Parallel for? I am attaching my Configuration file, pre.Parallel, post.Parallel, and Parallel to this message as well.
OS: Centos 7, Freesurfer version: 7.2.0
Thank you for your help. Kindly, Ela
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