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mriqc-cheatsheet.md

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MRIQC on biowulf

Building singularity images from docker hub

singularity build mriqc-0.16.simg docker:poldracklab/mriqc:0.16.1

Setting the SINGULARITY_BINDPATH env variable

export SINGULARITY_BINDPATH=/gs4,/gs6,/gs7,/gs8,/gs9,/gs10,/gs11,/spin1,/fdb,/data,/lscratch

Running mriqc

singularity run --cleanenv \
-B /data/NIMH_scratch/afni-frontiers-proj/ds-frontiers-qc:/in \
-B /data/NIMH_scratch/afni-frontiers-proj/ds-frontiers-qc/derivatives:/out \
/data/MLDSST/containers/mriqc-0.16.simg \
/in /out participant --participant_label 101