heudiconv_test.sh

#!/bin/bash

# if number of arguments is not 2
if [ $# -ne 2 ]
    then
    echo "Two arguments are required:"
    echo "1: name of the dicom directory (inputs)"
    echo "2: subject index"
    echo "e.g., ./heudiconv_test.sh Yuexin_project 01"
    echo "Prerequisites:"
    echo "Docker and heudiconv (docker image) are installed/built"
    echo "You should cd to the parent directory of the dicom directory (and bids directory if exists)"
    exit 1
fi

dicom_dir=${1}
isubject=${2}

# Must remove existing .heudiconv/ before another execution
sudo rm -rf ./${dicom_dir}_BIDS/

: '
## loop through all folders
## If multiple runs exist, outputs from older runs are replaced by those from later runs
cd ./${dicom_dir}/sub-${isubject}/

list_of_folder=(*)

cd ../../

length=${#list_of_folder[@]}

for (( i=0; i<$length; i++))
do 
    printf "\n Now processing ${list_of_folder[i]} \n"
    sudo rm -rf /home/yuexin/Documents/TestData/Yuexin_BIDS2/.heudiconv/01
    docker run --rm -it -v ${PWD}:/base nipy/heudiconv:latest -d /base/${dicom_dir}/sub-{subject}/${list_of_folder[i]}/*.dcm -o /base/${bids_dir}/ -f /base/${converter} -s ${isubject} -c dcm2niix -b --overwrite --minmeta
done
'

: '
## one folder
printf "\n Now processing ${list_of_folder[11]} \n"
docker run --rm -it -v ${PWD}:/base nipy/heudiconv:latest -d /base/${dicom_dir}/sub-{subject}/${list_of_folder[11]}/*.dcm -o /base/${bids_dir}/ -f /base/${converter} -s ${isubject} -c dcm2niix -b --overwrite --minmeta
'

## all in one folder command
printf "\n Now processing ${dicom_dir} sub-${isubject} \n"
docker run --rm -it -v ${PWD}:/base yuexinxi/heudiconv:latest --files /base/${dicom_dir}/sub-${isubject}/ -o /base/${dicom_dir}_BIDS/ -f heuristic_sequence -s ${isubject} -c dcm2niix -b --overwrite --minmeta