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





From: Yendiki, Anastasia

Sent: Mon, 06 Jun 2022 20:17:47 -0700

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




From:Yendiki, Anastasia

Fri, 03 Jun 2022 12:24:56 -0700




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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