s1_preprocess_data.sh

## PREPROCESS DATA, including:
#   1. conversion to BIDS
#   2. Defacing
#   3. MRIQC
#   4. FMRIPrep

# Exit upon any error
set -euo pipefail


## Change lines for Study/subject/system. Also add lines for stim files, TSV fles, and eye tracking files. Then try running it on our sample data.
DIRN=`dirname $0`
source $DIRN/setup.sh ${1-}
source "$CODE_DIR"/Subroutines/utils.sh


# Go!
# Sample data from subject wlsubj042, acquired on DATE!?!?!?!
#

###   Global variables:   ###

# Study/subject specific #
dcmFolder="$SAMPLE_DATA_DIR/dicoms"
logFolder=${LOG_DIR}/s1

mkdir -p $logFolder

fsLicense=$(fsLicensePath)


# we'll be running the Docker containers as yourself, not as root:
userID=$(id -u):$(id -g)


###   Get conatiner images:   ###
container_pull cbinyu/heudiconv:v3.7.0
container_pull bids/validator:v1.7.2
container_pull cbinyu/bids_pydeface:v2.0.3
container_pull poldracklab/mriqc:0.16.1
container_pull nipreps/fmriprep:20.2.3


# Set up some derived variables that we'll use later:
fsLicenseBasename=$(basename $fsLicense)
fsLicenseFolder=${fsLicense%$fsLicenseBasename}


###   Extract DICOMs into BIDS:   ###
# The images were extracted and organized in BIDS format:
# --name heudiconv_container \
container_run \
           $dcmFolder:/dataIn:ro \
           $STUDY_DIR:/dataOut \
           cbinyu/heudiconv:v3.7.0 \
           ${SINGULARITY_PULLFOLDER}/heudiconv_v3.7.0.sif \
               "-d /dataIn/{subject}/*/*.dcm \
               -f cbi_heuristic_simple \
               -s ${SUBJECT_ID} \
               -ss ${SESSION_ID} \
               -c dcm2niix \
               -b \
               -o /dataOut \
               --overwrite" \
           > ${logFolder}/sub-${SUBJECT_ID}_extraction.log 2>&1

# heudiconv makes files read only
#    We need some files to be writable, eg for defacing
chmod -R u+wr,g+wr ${STUDY_DIR}

## We run the BIDS-validator:

container_run \
           $STUDY_DIR:/data:ro \
           $STUDY_DIR:/ignore:ro \
           bids/validator:v1.7.2 \
           ${SINGULARITY_PULLFOLDER}/validator_v1.7.2.sif \
               "/data" \
           > ${logFolder}/bids-validator_report.txt 2>&1                   
           # For BIDS compliance, we want the validator report to go to the top level of derivatives. But for debugging, we want all logs from a given script to go to a script-specific folder
           #> ${STUDY_DIR}/derivatives/bids-validator_report.txt 2>&1



###   Deface:   ###
# The anatomical images were defaced using PyDeface:
container_run \
           $STUDY_DIR:/data \
           $STUDY_DIR:/ignore:ro \
           cbinyu/bids_pydeface:v2.0.3 \
           ${SINGULARITY_PULLFOLDER}/bids_pydeface_v2.0.3.sif \
               "/data \
               /data/derivatives \
               participant \
               --participant_label ${SUBJECT_ID} \
	       --skip_bids_validator" \
           > ${logFolder}/sub-${SUBJECT_ID}_pydeface.log 2>&1

###   MRIQC:   ###
# mriqc_reports folder contains the reports generated by 'mriqc'
container_run \
           $STUDY_DIR:/data \
           $STUDY_DIR:/ignore:ro \
           cbinyu/mriqc:0.15.0 \
           ${SINGULARITY_PULLFOLDER}/mriqc_0.16.1.sif \
               "/data \
               /data/derivatives/mriqc_reports \
               participant \
               --ica \
               --verbose-reports \
               --fft-spikes-detector \
               --participant_label ${SUBJECT_ID}" \
           > ${logFolder}/sub-${SUBJECT_ID}_mriqc_participant.log 2>&1
           
container_run \
           $STUDY_DIR:/data \
           $STUDY_DIR:/ignore:ro \
           cbinyu/mriqc:0.15.0 \
           ${SINGULARITY_PULLFOLDER}/mriqc_0.16.1.sif \
               "/data \
               /data/derivatives/mriqc_reports \
               group" \
           > ${logFolder}/sub-${SUBJECT_ID}_mriqc_group.log 2>&1

###   fMRIPrep:   ###
# fmriprep folder contains the reports and results of 'fmriprep'
container_run \
           $STUDY_DIR:/data \
           ${fsLicenseFolder}:/FSLicenseFolder:ro \
           nipreps/fmriprep:20.2.1 \
           ${SINGULARITY_PULLFOLDER}/fmriprep_20.2.1.sif \
               "/data \
               /data/derivatives \
               participant \
               --fs-license-file /FSLicenseFolder/$fsLicenseBasename \
               --output-space T1w:res-native fsnative:res-native \
               --participant_label ${SUBJECT_ID} \
               --skip_bids_validation \
               --no-submm-recon" \
           > ${logFolder}/sub-${SUBJECT_ID}_fMRIPrep.log 2>&1