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Add --use-aroma

STAR-pipeline/slurm-fmriprep.sh

Line 17 in 50fa590

singularity run --cleanenv -B /mnt/stressdevlab/STAR /mnt/stressdevlab/scripts/Containers/fmriprep-${VERSION}.simg/ --ignore slicetiming --participant-label ${SUBJECT} -vvv --nthreads 4 -w ${SCRATCH}/fmriprep-${VERSION}-test2/${SUBJECT} --return-all-components --fd-spike-threshold 0.5 --fs-license-file /mnt/stressdevlab/STAR/derivatives/license.txt --fs-subjects-dir /mnt/stressdevlab/STAR/derivatives/fmriprep-${VERSION}/freesurfer --cifti-output 91k --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym fsnative MNIPediatricAsym:cohort-1:res-2 --skip-bids-validation /mnt/stressdevlab/STAR /mnt/stressdevlab/STAR/derivatives/fmriprep-${VERSION} participant

We should add this option in case anyone wants to use ICA-AROMA confound removal, which works best for certain resting-state analyses.

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