cbu2bids_nodeface

#!/bin/bash
#
# CBU wrapper for dcm2bids. Takes care of adding code to path and setting the
# correct python / PYTHONPATH. This variant omits de-facing of the structural
# images - be sure that this is what you want.
#
# 2018-10-18 J Carlin

export PATH=/imaging/local/software/dcm2niix/bin:$PATH
export PATH=/imaging/local/software/fsl/fsl64/fsl-5.0.3/fsl/bin/:$PATH
export PATH=/imaging/local/software/anaconda/2.4.1/2/envs/heudiconv/bin/:$PATH
export PATH=/imaging/local/software/dcm2bids/scripts:$PATH
export PYTHONPATH=/imaging/local/software/dcm2bids
export FSLOUTPUTTYPE=NIFTI_GZ

# need to make sure outputdir is set to avoid attempts to write to script dir
# (which will be cwd in dcm2bids below)
validcheck=0
for var in "$@"
do
    if [[ $var == -o ]]; then
        validcheck=1
    fi
    if [[ $var == --outputdir ]]; then
        validcheck=1
    fi
done
if [ $validcheck == 0 ]; then
    echo "ERROR: must specify outputdir by setting -o or --outputdir flag"
    exit 1
fi

# bash voodoo for pass any and all input arguments on
dcm2bids "$@"