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Instructions


SITE_TIMEZONES

(complete list is here: http://tutorials.jenkov.com/java-date-time/java-util-timezone.html)

In ECAT you have to know the timezone in which the scan was acquired in order to extract the correct time and date of the scan. You will need to know in which timezone each ECAT was scanned if possible.

This is just an example properties file, ${SITE_TIMEZONES}, I use to figure out which timezone the ecat is from. I get the acquisition site (not always the same as the site in which subject is enrolled), and then I get the timezone.
DIAN_011:America/Chicago
DIAN_024:America/New_York
DIAN_035:America/Los_Angeles
DIAN_037:America/New_York
DIAN_094:America/New_York
DIAN_953:Europe/London
timezone=`cat ${SITE_TIMEZONES} | grep ${acqSite} | cut -d: -f2`
echo timezone $timezone
TIMESTAMP
You need a timestamp simply to provide a unique directory name for the CNDA ADNI_PROC prearchive space.
Below is how I get timestamp in the right format.
timestamp=`date +%Y%m%e_%k%M%S`
echo timestamp $timestamp
REST UPLOAD
Step 1: Upload each scan in the session as a zip to your timestamp directory.

for each $scannum in $cndaSessionLabel
curl -k -b JSESSIONID=$JSESSION -F "${ecatScanFiles}.zip=@${ecatScanFiles}.zip" -X POST "https://cnda.wustl.edu/data/services/import?dest=/prearchive/projects/A_PROJECT/${timestamp}/${cndaSessionLabel}&TIMEZONE=${timezone}&SOURCE=scriptName&SUBJECT_ID=${cndaSubjectLabel}&label=ECAT&format=ECAT&content=RAW&overwrite=append&xnat:petSessionData/scans/scan/ID=${scannum}&extract=true"

Step 2: Tell CNDA you're finished uploading for this session and to do a build to create metadata in prearchive for session.
curl -k -b JSESSIONID=$JSESSION -X POST "https://cnda.wustl.edu/data/prearchive/projects/A_PROJECT
/${timestamp}/${cndaSessionLabel}?action=commit&SOURCE=scriptName&TIMEZONE=${timezone}"