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fmriprep-slurm
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Generate and run SLURM jobs on HPCs
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fmriprep-slurm
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# fmriprep-slurm Generate and run [fMRIPrep](https://fmriprep.org/en/stable/) [SLURM](https://slurm.schedmd.com/documentation.html) jobs on HPCs. It is carefully designed and optimized to run the preprocessing on a [BIDS](https://bids-specification.readthedocs.io/en/stable/) dataset. It has also the advantage to prepare the dataset by checking the integrity, and caching some of the BIDS database artifacts. Originally from https://github.com/courtois-neuromod/ds_prep/blob/master/derivatives/fmriprep/fmriprep.py ## Usage ### Arguments ``` positional arguments: bids_path BIDS folder to run fmriprep on. derivatives_name name of the output folder in derivatives. optional arguments: -h, --help show this help message and exit --preproc PREPROC anat, func or all (default: all) --slurm-account SLURM_ACCOUNT SLURM account for job submission (default: rrg-pbellec) --email EMAIL email for SLURM notifications --container CONTAINER name of the fmriprep singularity container under the default container location (default: fmriprep-20.2.1lts) --participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...] a space delimited list of participant identifiers or a single identifier (the sub- prefix can be removed) --output-spaces OUTPUT_SPACES [OUTPUT_SPACES ...] a space delimited list of templates as defined by templateflow (default: ["MNI152NLin2009cAsym, MNI152NLin6Asym"]) --fmriprep-args FMRIPREP_ARGS additionnal arguments to the fmriprep command as a string (ex: --fmriprep-args="--fs-no-reconall --use-aroma") --session-label SESSION_LABEL [SESSION_LABEL ...] a space delimited list of session identifiers or a single identifier (the ses- prefix can be removed) --force-reindex Force pyBIDS reset_database and reindexing --submit Submit SLURM jobs --bids-filter BIDS_FILTER Path to an optionnal bids_filter.json template --time TIME Time duration for the slurm job in slurm format (dd-)hh:mm:ss (default: 24h structural, 12h functionnal) --mem-per-cpu MEM_PER_CPU upper bound memory limit for fMRIPrep processes(default: 4096MB) --cpus CPUS maximum number of cpus for all processes(default: 16) ``` Templateflow valid identifiers can be found at https://github.com/templateflow/templateflow ## Default fmriprep command By default, we use the following fMRIPrep arguments: `--participant-label` dependning on the user argument choice. `--bids-database-dir` which takes as an input the cached from pybids. `--bids-filter-file` dependning on the user argument choice. `--notrack` since beluga compute nodes does not have access to internet, and reduce computation burden. `--skip_bids_validation` since it was already done inside `fmriprep-slurm`. `--write-graph` for debugging. `--omp-nthreads`, `--nprocs` and `--mem_mb` dependning on the user argument choice. `--resource-monitor` for debugging. For more information on each of these option, you can check the [documentation](https://simexp-documentation.readthedocs.io/en/latest/giga_preprocessing/preprocessing.html).
