While pre-processing resting state fMRI data, I tried to limit the processing done in parallel, since my cluster allows only for a limited amount of capacity used. Therefore, I wanted to use the implemented parameter '--n-jobs' of the 'generic-prep' function. Unfortunately, I couldn't manage to let the parameter be accepted.
I tried my basic code
SAMRI generic-prep -n-jobs 4 -o Exp1 -f '{"acquisition":["rsfMRI"],"subject":["169"]}' -s '{"acquisition":["FLASH"],"subject":["169"]}' Exp1/bids samriTemplates/dsurqec_200micron.nii
with various other options of -n-jobs that all led to the following error:
SAMRI: error: unrecognized arguments: -n-jobs samriTemplates/dsurqec_200micron.nii
Running this code without the n-jobs parameter leads to an error message:
Message from root@eu-login-10-ng on pts/2 at 10:40 ...
You are overloading this login node (2 threads N4BiasFieldCorr +
9 threads SAMRI + 1 thread python on 4 CPUS).
Please DO NOT use more than 4 threads + processes on login nodes !
Please use LSF, if you need more resources.
While pre-processing resting state fMRI data, I tried to limit the processing done in parallel, since my cluster allows only for a limited amount of capacity used. Therefore, I wanted to use the implemented parameter '--n-jobs' of the 'generic-prep' function. Unfortunately, I couldn't manage to let the parameter be accepted.
I tried my basic code
SAMRI generic-prep -n-jobs 4 -o Exp1 -f '{"acquisition":["rsfMRI"],"subject":["169"]}' -s '{"acquisition":["FLASH"],"subject":["169"]}' Exp1/bids samriTemplates/dsurqec_200micron.niiwith various other options of
-n-jobsthat all led to the following error:SAMRI: error: unrecognized arguments: -n-jobs samriTemplates/dsurqec_200micron.niiRunning this code without the n-jobs parameter leads to an error message: