Reusing derivatives in fMRIPrep in NeuroDesktop

Software Support
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1

Summary of what happened:

I have a rs-fMRI dataset with anatomical and functional data of approximately 1400 subjects. Which would be the standard or most optimal approach to preprocess the data in this case? Should I run fmriprep directly on the whole BIDS formatted dataset? Should I process each subject individually?

Additionally, is it possible to resume an fMRIPrep preprocessing run from a previously executed session?

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep \
  /home/jovyan/Desktop/DatasetOASIS3/raw \
  /home/jovyan/Desktop/DatasetOASIS3/derivatives \
  participant \
  --skip-bids-validation \
  --n-cpus 16 \
  --mem 240000 \
  --work-dir /home/jovyan/Desktop/DatasetOASIS3/work \
  --output-spaces MNI152NLin2009cAsym:res-2 \
  --bold2anat-init t2w \
  --cifti-output 91k \
  --fs-license-file /home/jovyan/Desktop/PBL_Neuro/Freesurfer/license.txt \
  --random-seed 34 \
  --notrack

Version:

25.1.3

Environment (Docker, Singularity / Apptainer, custom installation):

NeuroDesktop

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

2

Hi @Ibai_Azpeitia_Loiti,

fMRIprep automatically parallelizes with what resources are available. But if you are on a HPC, it is standard to have multiple jobs running to fully leverage the supercomputer parallelization.

Yes, just supply a working directory as you already are, and you can also use the --derivatives argument: Usage Notes — fmriprep version documentation

Best,
Steven

3

Perfect, thanks for the reply.