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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

XCP needs a Design file, and a Cohort file. The Design file specifies the processes that XCP will perform on the data.

The Cohort file lists all of the participants that the design file will apply the jobs to.

Run on TACC in scratch directory. Insert this code into terminal:
sbatch xcpCohort1.dms****

An example slurm job script is below: