dicom2nii_BIDS_Step2.sh

#!/usr/bin/env bash

# to run the script, open the terminal and run:
# sh./ dicom2nii_BIDS_Step2.sh

source config.sh

subjects=("AlSo" "BrCh")
subjects_numbers=("2" "3")

WD=`pwd`

cd ${bids_output_folder}

nb_subjects=${#subjects[@]}
echo 'Number of Subjects: '${nb_subjects}

# for loop that iterates over each element in arr
for iSub in "${!subjects[@]}" #{1..${nb_subjects}}
do

    sub_name="${subjects[${iSub}]}"
    sub_nb="${subjects_numbers[${iSub}]}"
    sub_nb="$(printf "%02d" ${sub_nb})"
    echo 'Subject Name:' ${sub_name} " - ID:"${sub_nb}

    # For every condition you have, add the following block of code to get the DICOM location

    ##############################################################################
    # dcm2bids inputs:
    #
    # dcm2bids -d ${sub_dicom_folder} \
    #          -p ${sub_label} \
    #          -s ${ses_label} \
    #          -c config.json \
    #          -o ${bids_output_folder}
    #
    # -d Dicom path
    # -p Partipiant label
    # -s Session label
    # -o Output directory for the nifti files
    # -c Configuration json file that should be present in the output directory
    ##############################################################################

    ## 1. ANAT
    # the directory to the dicom files (needs to be changed according to your dicom location and name)
    sub_dicom_folder=${dicoms_folder}'Anatomical/'${sub_name}           ## <---------- CHANGE THE LOCATION

    echo "DICOMS folder is: "${sub_dicom_folder}
    echo "Output folder is: "${bids_output_folder}

    dcm2bids -d ${sub_dicom_folder} \
    -p ${sub_nb} \
    -s 01 \
    -c ${config_file} \
    -o ${bids_output_folder}

    ## 2. FUNC
    taskName='visMotion'                                                ## <---------- CHANGE THE TASK NAME

    sub_dicom_folder=${dicoms_folder}'Control/'${sub_name}              ## <---------- CHANGE THE LOCATION

    echo "DICOMS folder is: "${sub_dicom_folder}
    echo "Output folder is: "${bids_output_folder}

    dcm2bids -d ${sub_dicom_folder} \
    -p ${sub_nb} \
    -s 01 \
    -c ${config_file} \
    -o ${bids_output_folder}

    ### remove dummies
    file=${bids_output_folder}'/sub-'${sub_nb}'/ses-01/func/sub-'${sub_nb}'_ses-01_task-'${taskName}'_bold.nii.gz'
    echo ${file}
    cd $WD
    python remove_dummies.py ${file} ${number_dummies} ${delete_original}
    cd ${bids_output_folder}

    ## 3. ADD OTHER EXPERIMENTS IF NEEDED BY COPYING ONE OF THE ABOVE

done