xnat_import_nifti

#!/bin/bash

PROJECT=$1
SUBJECT=$2
SESSION=$3
SCAN_TYPE=$4
NIFTI=$5
SESSION_DATE=$6

if [[ "$SCAN_TYPE" == "T1" ]]; then
    SCAN_NUM="001"
else
    SCAN_NUM="002"
fi

output='&> /dev/null'

# check if enough args
if [[ $# -lt 5 ]]; then
    echo "Usage: $(basename $0) project subject session scan-type nifti-file [mm/dd/yy]"
    echo ""
    echo "This tool should be used when: "
    echo "  * dicom files do NOT exist "
    echo "  * nifti files ARE available"
    echo "  * project already exists within XNAT"
    exit 0;
fi


if [[ $SESSION_DATE == "" ]]; then
    SESSION_DATE=$(date +"%m/%d/%y")
fi

# project URI
uri_project="/data/archive/projects/${PROJECT}"
uri_subject="$uri_project/subjects/${SUBJECT}"
uri_session="$uri_subject/experiments/${SESSION}"
uri_scan="$uri_session/scans/$SCAN_NUM"

# create subject (if does not already exist)
XNATRestClient -tsPass -m PUT -remote "$uri_subject" $output

# create session (if does not already exist)
XNATRestClient -tsPass -m PUT -remote "${uri_session}?xnat:mrSessionData/date=${SESSION_DATE}" $output

# create scan
XNATRestClient -tsPass -m PUT -remote "${uri_scan}?xsiType=xnat:mrScanData&xnat:imageScanData/type=$SCAN_TYPE" $output

# upload file
XNATRestClient -tsPass -m PUT \
               -local  $NIFTI \
               -remote "${uri_scan}/resources/NIFTI/files/$SCAN_NUM.nii.gz?format=NIFTI&content=NIFTI_RAW" $output