hi lea,

in addition you could consider using the bids app for freesurfer: https://github.com/BIDS-Apps/freesurfer

and then submit each subject's longitudinal pipeline as a separate slurm job.

cheers,

satra

On Thu, Feb 22, 2018 at 10:43 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu

wrote:

Hi Lea,

I wrote that script to simplify processing on our cluster which uses qsub PBS for submission. I have never used SLURM so far.

There is two functions that you (or someone who knows this stuff) would need to modify:

def submit

and

def wait_jobs

The submit procedure basically issues a submit command (stored in pbcmd). The examples there should help anyone who programs python to modify it for a slurm submission.

The wait_jobs scripts runs a different command (here qstat and grep user) to see how many jobs you are already running and waits until this number sinks below maxjobs, then it continues submitting new jobs. If you don't care about the number of submitted jobs (because your cluster does the scheduling anyway), you can just write

" return" as the first line (before the " users = os....." line).

Still the submit block would have to be rewritten for slurm.

Best, Martin

Am 17.02.2018 um 12:13 schrieb Backhausen, Lea:

Dear FS experts,

I am trying to do a longitudinal analysis of around 250 adolescents with up to 4 data points each. Given the complexity I would like to use the long_submit_jobs script which is described here: https://surfer.nmr.mgh. harvard.edu/fswiki/FsTutorial/Scripts

Unfourtunately it does only run on launchpad and I would do the analyses with SLURM using bash system. Has anybody adopted the script so i will run with SLURM or does anybody know where I should look to get information on this?

I have little scripting experience so any help would be greatly appreciated!

Best,

Lea Backhausen, B.Sc.

Research assistant

Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie Tel. +49 (0)351 458-7166 <+49%20351%204587166> Fax +49 (0)351 458-5754 <+49%20351%204585754>

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