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Welcome to the Attention-Bias-Modification-R33-Clinical-Trial wiki!

BIDS-aps.

BIDS-app typically require Docker if they are being run on a local computer, or Singularity if they are being run on TACC.

MRIQC

Quality Control - used to quantify the amount of motion in functional MRI data.
https://mriqc.readthedocs.io/en/stable/

To run QC on an individual subject:
docker run -it --rm -v /Users/PSYC-klr3342/Documents/R33_RAW/testBIDS/:/data:ro -v /Users/PSYC-klr3342/Documents/R33_RAW/MRIQC/:/out poldracklab/mriqc:0.9.10 /data /out participant --participant_label sub-16750 --no-sub --fd_thres 0.25 -vvv --session-id 03.

To get a group summary of the BIDS dataset:
docker run -it --rm -v /Volumes/schnyer/R33ABM/testBIDS/:/data:ro -v /Volumes/schnyer/R33ABM/MRIQC/:/out poldracklab/mriqc:0.9.10 /data /out group

fMRIprep

Preprocessing - used to align functional data to structural scans and then register to MNI template.
Also extracts many motion and other confounds that can be potential removed from data.
https://fmriprep.readthedocs.io/en/stable/

Insert this code into terminal:
./Library/Python/3.6/lib/python/site-packages/fmriprep_docker.py /Users/PSYC-klr3342/Documents/R33_RAW/testBIDS /Users/PSYC-klr3342/Documents/R33_RAW/fMRIprep participant --participant-label sub-11985 --ignore slicetiming -t REST --fs-license-file /Users/PSYC-klr3342/Downloads/license.txt --fs-no-reconall --debug

XCP

Used to process fMRI data, picks up where fMRIprep left off.
https://xcpengine.readthedocs.io