main

#!/bin/bash
## stuff from jobheader.sh
#PBS -N qsiprep

set -x
set -e

export FREESURFER_LICENSE="hayashis@iu.edu 29511 *CPmh9xvKQKHE FSg0ijTusqaQc"
echo $FREESURFER_LICENSE > license.txt

bl2bids

WORKDIRNAME=$(pwd)/qsipworkdir
outdir=$(pwd)/output

resolution=$(jq -r .output_resolution config.json) 
space=$(jq -r .output_space config.json) 
template=$(jq -r .template config.json) 
#sub=$(jq -r '._inputs[] | select(.id == "t1w") | .meta.subject' config.json)
sub=$(jq -r '._inputs[0].meta.subject' config.json)
dwi=$(jq -r .dwi config.json)
skipbidsvalidation=$(jq -r .skipbidsvalidation config.json)
denoise_method=$(jq -r .denoise_method config.json)
distortion_group_merge=$(jq -r .distortion_group_merge config.json)
unringing_method=$(jq -r .unringing_method config.json)
hmc_transform=$(jq -r .hmc_transform config.json)
infant=$(jq -r .infant config.json)
syn_sdc=$(jq -r .syn_sdc config.json)
force_syn=$(jq -r .force_syn config.json) #keep to be back compatible
check_flip_bvecs=$(jq -r .check_flip_bvecs config.json)
#reconall=$(jq -r .reconall config.json)

optional=""

if [[ $dwi == *","* ]]; then 
	echo "Multi dwi input found. Distortion group merge option: ${distortion_group_merge}"; 
	optional="$optional --distortion-group-merge ${distortion_group_merge}";	
fi

if [[ $space == "MNI152NLin2009cAsym" ]]; then 
	echo "Sampling T1w, brain mask, and parcellation/volume to MNI152NLin2009cAsym space."; 
	optional="$optional --template MNI152NLin2009cAsym";	
fi

# boolean options
[ $skipbidsvalidation == "true" ] && optional="$optional --skip-bids-validation"
[ $infant == "true" ] && optional="$optional --infant"
[ $syn_sdc == "true" ] && optional="$optional --use-syn-sdc --force-syn"
#[ $reconall == "true" ] && optional="$optional --do-reconall"
    
# remove if stuff already exists
rm -rf $WORKDIRNAME && mkdir -p $WORKDIRNAME
rm -rf $outdir && mkdir -p $outdir

## EXPERIMENTAL: try to use freesufer input
## removing the following since it's not used in the preprocessing workflow
#inFSDIR=`jq -r '.fsin' config.json`
#
#if [[ $inFSDIR != "null" ]] ; then
#
#    #clean up previous freesurfer dir if it exists
#    rm -rf $outdir/freesurfer
#    mkdir -p $outdir/freesurfer
#
#    #TODO - strip alphanumeric chars?
#    cp -rH $inFSDIR $outdir/freesurfer/sub-$sub
#    chmod -R +rw $outdir/freesurfer

#    #run reconall to get the fsaverage folder - 
#    #it should recognize though the folder just created
#    if $reconall == "false"; then
#        optional="$optional --do-reconall"
#    fi
#fi

# avoid templateflow problems on HPC's running singularity
mkdir -p templateflow
export SINGULARITYENV_TEMPLATEFLOW_HOME=$PWD/templateflow

# set FreeSurfer
[ -z "$FREESURFER_LICENSE" ] && echo "Please set FREESURFER_LICENSE in .bashrc" && exit 1;

# check and flip bvecs if needed (actually not needed since qsiprep should check it)
#if [[ $check_flip_bvecs == "true" ]]; then 
#	echo "check if bvecs need to be flipped - flip them if necessary"
#	./check_and_flip_bvecs.sh
#fi

# QSIPrep
time singularity exec -e \
    docker://pennbbl/qsiprep:0.14.2 \
    /usr/local/miniconda/bin/qsiprep \
    --fs-license-file license.txt \
    --output-resolution $resolution \
    --denoise-method $denoise_method \
    --unringing-method $unringing_method \
    --hmc-transform $hmc_transform \
    --nthreads 8 \
    --verbose \
    --work-dir $WORKDIRNAME \
    bids $outdir participant \
    $optional
    
echo "done with qsiprep! - now organizing output"
./qsiprep2bl.sh

rm -r $WORKDIRNAME # save lots of space    

echo "all done!"