SHOREline Iteration registration error

[aiims-himanshu]

Hi, I have an irregular error that occurs at 1/6-7 preprocessing subjects, it is across SHORELine itreation predicted value registration were in certain predicted variable are not found in the directories, My line of code.

QSIprep preprocessing (315m/subject)

sudo docker run -ti --rm \ -v /media/himanshu/m2/test1/input:/data:ro \ -v /media/himanshu/m2/test1/output:/out \ -v /media/himanshu/m2/test1/tmp1:/w \ -v /home/himanshu/freesurfer/:/freesurfer \ pennbbl/qsiprep \ /data /out \ participant \ -w /w \ --fs-license-file /freesurfer/license.txt \ --verbose \ --dwi_denoise_window auto \ --denoise_method dwidenoise \ --unringing_method mrdegibbs \ --b0-to-t1w-transform Affine \ --hmc-transform Affine \ --hmc_model 3dSHORE \ --shoreline_iters 5 \ --b0-motion-corr-to iterative \ --skull-strip-template NKI \ --skull-strip-fixed-seed \ --fmap-bspline \ --force-syn \ --output-space T1w \ --output_resolution 2 \ --write_graph \ --notrack

System is 16 Core, 128 GB RAM and Space 1.8/7.4 TB,

Following error is not regular however it does occur at certain instances. Rerun twice or thrice solve the issue. Data is BIDS format. first crash- register 24-62 second crash- register 11

just recently started using fmriprep/qsiprep pipeline in last few months.

crash-20220710-135102-root-_register_to_predicted24-62fdd037-2403-4be0-9843-22df4a51b913.txt crash-20220710-155944-root-_register_to_predicted11-f2d5f1a9-ef0a-4be3-aace-49bb0c659121.txt

[mattcieslak]

Hi! I think you should regulate CPU usage. Maybe something like adding --nthreads 15 --omp-nthreads 3

[aiims-himanshu]

Hi, CPU regulation resolved the issue as of now completed 5 subjects with the command running the second batch with 8, i restricted nthreads 14, and omp-nthreads came down to 8 (Automatically). also following aspect helped to reduce preprocessing time by 30% in my case with batch process taking 5 subjects at a time.

Thanks