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bids_conversion_bdrive.sh
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#!/bin/bash
###############################################################################
####################### STEP 1: DOWNLOAD XNAT DICOM DATA ######################
###############################################################################
# CHANGE THE NEXT TWO LINES
range_subject="62" # "0-1" will download the first 2 subjects
num_subject=1 # CHANGE THIS
echo "Start downloading XNAT data for" $num_subject "participant(s)"
script_dir=/Users/TienTong/Documents/dcm2bids
$script_dir/xnat_download.py \
--range_subject $range_subject \
--username `sed -n 1p $script_dir/credentials.txt` \
--password `sed -n 2p $script_dir/credentials.txt` \
--download_dir /Volumes/BACHI-LAB/MRI_DATA/DICOM
###############################################################################
################### STEP 2: CONVERT TO NIFTY AND PUT IN BIDS ##################
###############################################################################
export DICOM="/Volumes/BACHI-LAB/MRI_DATA/DICOM"
export BIDS="/Volumes/BACHI-LAB/MRI_DATA/BIDS"
script_dir=/Users/TienTong/Documents/dcm2bids
new_download=($(ls -d "$DICOM"/*))
for i in ${!new_download[@]} ; do
subject_id=`echo ${new_download[$i]} | awk -F "_" '{print $NF}'`
mv ${new_download[$i]} "$DICOM"/${subject_id}
rm -rf "$BIDS"/tmp_dcm2bids
################### STEP 2.1a: CONVERT TO NIFTY AND PUT IN BIDS ############
echo "Start doing BIDS conversion for subject" ${subject_id}
dcm2bids \
-d "$DICOM"/${subject_id}/*/scans \
-p ${subject_id} \
-c /Users/TienTong/Documents/dcm2bids/dcm2bids_config.json \
-o "$BIDS" \
--clobber --forceDcm2niix
# need to add task name to .json file. eg: "TaskName": "${task}"
# need to add IntendedFor for fmap
######################## STEP 2.1b: RENAME FILES ###########################
# run and echo were flipped using dcm2bids, have to switch them back
subject_func="$BIDS"/sub-${subject_id}/func
for task in rest whyhow ; do
task_list=($(ls $subject_func/*${task}*bold.nii.gz))
run_num=$((${#task_list[@]} / 3))
if [ $run_num -gt 1 ] ; then
for run in `seq -s " " -f "%02g" $run_num` ; do
for echo in 01 02 03 ; do
for type in bold sbref ; do
for extension in json nii.gz ; do
old=$subject_func/sub-${subject_id}_task-${task}_echo-${echo}_run-${run}_${type}.${extension}
new=$subject_func/sub-${subject_id}_task-${task}_run-${run}_echo-${echo}_${type}.${extension}
mv $old $new
done
done
done
done
fi
done
echo "BIDS conversion completed for subject" ${subject_id}
################### STEP 2.2: RUN OPTIMAL COMBINATION #####################
for task in rest whyhow ; do
task_list=($(ls $subject_func/*${task}*bold.nii.gz))
run_num=$((${#task_list[@]} / 3))
echo "Start the tedana optimal combination for" $run_num "run(s) of the" ${task} "task of subject" ${subject_id}
if [ $run_num -gt 1 ] ; then
for run in `seq -s " " -f "%02g" $run_num` ; do
input=(`ls $subject_func/*${task}*run-${run}*bold.nii.gz`)
t2smap \
-d ${input[@]} \
-e 10.80 28.68 46.56 \
--out-dir $subject_func
rm $subject_func/*S0map* $subject_func/*T2starmap*
mv $subject_func/desc-optcom_bold.nii.gz $subject_func/sub-${subject_id}_task-${task}_run-${run}_bold.nii.gz
cp $subject_func/sub-${subject_id}_task-${task}_run-${run}*echo-01*_bold.json $subject_func/sub-${subject_id}_task-${task}_run-${run}_bold.json
done
else
input=(`ls $subject_func/*${task}*bold.nii.gz`)
t2smap \
-d ${input[@]} \
-e 10.80 28.68 46.56 \
--out-dir $subject_func
rm $subject_func/*S0map* $subject_func/*T2starmap*
mv $subject_func/desc-optcom_bold.nii.gz $subject_func/sub-${subject_id}_task-${task}_bold.nii.gz
cp $subject_func/sub-${subject_id}_task-${task}*echo-01*_bold.json $subject_func/sub-${subject_id}_task-${task}_bold.json
fi
# need to delete echo time of the optimally combined bold
done
###############################################################################
############################ STEP 3: MODIFY JSON FILES ########################
###############################################################################
# need to add task name to .json file. eg: "TaskName": "${task}"
# need to add IntendedFor for fmap
# need to delete echo time of the optimally combined bold
$script_dir/modify_json.py \
--subject ${subject_id} \
--bids_path "$BIDS"
done