gistfile1.txt

usage: micc-fmriprep.py [-h] [--aroma] [--disable-syn-sdc] [--ncpus NCPUS]
                        [--ramsize RAMSIZE] [--freesurfer] [--anat-only]
                        [--output-spaces OUTPUT_SPACES] --bidsdir BIDSDIR
                        --outputdir OUTPUTDIR --workdir WORKDIR --participant
                        PARTICIPANT [--fmriprep-container FMRIPREP_CONTAINER]

Run fMRIPrep, with some MIC cluster specific presets.

optional arguments:
  -h, --help            show this help message and exit
  --aroma               Turn on AROMA processing. (Default: off)
  --disable-syn-sdc     Turn OFF synthetic field map correction. (Default: on)
  --ncpus NCPUS         Number of threads and cores. (Default: 4)
  --ramsize RAMSIZE     RAM size to use, in GB. (Default: 8)
  --freesurfer          Enable FreeSurfer processing. (Default: off)
  --anat-only           Do only anatomical processing - no fMRI.
  --output-spaces OUTPUT_SPACES
                        Specify the output space. Enclose it in double
                        quotes.Default: "MNI152NLin6Asym:res-2 anat func
                        fsaverage"

required arguments:
  --bidsdir BIDSDIR     BIDS directory.
  --outputdir OUTPUTDIR
                        Output directory.
  --workdir WORKDIR     Work directory.
  --participant PARTICIPANT
                        Participant label.

You don't need to touch these:
  --fmriprep-container FMRIPREP_CONTAINER
                        Path to the fMRIPrep container. Default:
                        "/cm/shared/singularity/images/fmriprep-1.4.1.simg"