UPLOAD MULTI SUBJECTS / SESSION XNAT

Following the same line of work as the last blog post, I'll explain a possible way of uploading a set of Dicom images separated in folders indicating subject/session organization into XNAT. This solution is based on a script by Hauke Bartsch (hbartsch@ucsd.edu).

Bash script

The script uses XNAT's REST API to upload DICOM files organized by subject and session folders. It creates sessions and subjects as needed, then uploads the files in bulk.

# Create a session cookie, we want to re-use that session instead of 
# providing login information every time. Number of sessions might be 
# limited otherwise to 1000.

cookie=`curl -k -u $USER:$PASSWORD -X POST $XNAT/data/JSESSION`
echo "Session ID is: $cookie"

# create subject in case it does not exist
echo "create subject $c"
c=`curl --cookie JSESSIONID=$cookie -k -X PUT \
    $XNAT/data/archive/projects/$PROJECT/subjects/$subject`

# create session in case it does not exist
echo "create session $c"
c=`curl --cookie JSESSIONID=$cookie -k -X PUT \
    $XNAT/data/archive/projects/$PROJECT/subjects/$subject/\
experiments/$session?xsiType=xnat:mrSessionData`

timestamps=( )
for file in `find $directory -type f -print`
do
    # move file over using REST API
    c=`curl --cookie JSESSIONID=$cookie -s -k \
        -H 'Content-Type: application/dicom' \
        -X POST "$XNAT/data/services/import?\
inbody=true&PROJECT_ID=$PROJECT&SUBJECT_ID=$subject&\
EXPT_LABEL=$session&prearchive=true&overwrite=append&\
format=DICOM&content=T1_RAW" \
        --data-binary @$file | tr -d [:cntrl:]`
    
    echo -n "."
    timestamp=`echo $c | cut -d'/' -f6`
    
    # is timestamp new?
    found="0"
    for f in "${timestamps[@]}"; do
        if [ "$f" = "$timestamp" ]; then
            found="1"
        fi
    done
    
    # add to array
    if [ $found = "0" ]; then
        timestamps+=($timestamp)
        echo "found a new series $timestamp"
    fi
done

echo "done sending files..."

Key Points

• Session cookies are reused to avoid hitting session limits
• Subjects and sessions are created automatically if they don't exist
• Files are uploaded using XNAT's REST API with DICOM content type
• Timestamps track unique series to avoid duplicates

This script allows batch uploading of DICOM images organized in a folder structure, making it easy to populate XNAT with large datasets without manual intervention.