#!/bin/bash

#User inputs:
bids_root_dir=/my/bids_root_dir
Subjlist="N1098"
#nthreads=4
#mem=20 #gb
container=docker

#Begin:
export FS_LICENSE=/home/brain/freesurfer/7.3.2/license.txt

#Run QSIprep
if [ -n "${command_line_specified_subj}" ]; then
		Subjlist="${command_line_specified_subj}"
fi
	# Cycle through specified subjects
	for Subject in $Subjlist ; do
		echo $Subject 
		qsiprep-docker $bids_root_dir $bids_root_dir/derivatives/qsiprep \
		participant \
		-w /mnt/data/qsiprep/ \
		  --skip-bids-validation \
		  --participant-label $Subject \
		  --output-resolution 2 \
		  --omp-nthreads 1 \
          	  --anat-modality T1w \
          	  --dwi_denoise_window auto \
          	  --denoise-method dwidenoise \
          	  --unringing-method mrdegibbs \
          	  --hmc-model eddy \
		  --eddy_config "/my/bids_root_dir/code/eddy_params.json" \
          	  --skull-strip-fixed-seed \
          	  --fs-license-file $FS_LICENSE \
          	  --pepolar-method TOPUP \
		  --stop-on-first-crash \
          	  --notrack
	done