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Using fmriprep and MRIqc with docker on a UNIX machine#

Better to set in the terminal an absolute path to one-level-up the BIDS root in this way

#macOS
dataset_dir=one-level-up-BIDS-root

#Linux
export dataset_dir=one-level-up-BIDS-root

check that it worked

#macOS
$dataset_dir

#Linux
echo $dataset_dir

fmriprep#

useful and optional flags#

--verbose
--skip-bids-validation
--output-space anat
--fs-no-reconall
--participant-label pilot001

run#

fmriprep-docker \
$dataset_dir/raw \
$dataset_dir/derivatives \
-i nipreps/fmriprep:20.2.3 \
--fs-license-file $FREESURFER_HOME/license.txt \
--verbose \
--participant-label pilot001 \
--output-space anat

mriqc#

useful and optional flags#

run#

  • single participant
docker run -it --rm \
-v $dataset_dir/raw:/data:ro \
-v $dataset_dir/derivatives:/out \
poldracklab/mriqc:0.16.1 \
/data /out --no-sub --verbose-reports \
participant --participant-label pilot001
  • group
docker run -it --rm \
-v $input_dir:/data:ro \
-v $output_dir:/out \
poldracklab/mriqc:0.16.1 \
/data /out --no-sub --verbose-reports \
group

** OLD to tidy up **

https://neurostars.org/t/fmriprep-on-symlinked-bids-dataset/18025/13