How to use Docker containers in XNAT
To upload (Assuming you have already an xnat-project).
- Organise the DICOMs you want to upload into a structure like: mymaindirectory/
Where DICOMdir contains the DICOM data for a specific session for a certain subject (subject_ID)
- Create a .csv file (e.g. myproject.csv) with 3 columns:
|subject_ID | DICOMdir | scan_date | |————-|————|—————|
- subject_ID is uniquely associated with the participant
- directory is the name of the directory containing the DICOM files to upload. If more sessions of a certain subject exist, they have the code of the session (e.g. Calpendo ID)
- Run the csvupload.sh script:
./csvupload.sh myproject.csv <xnat-username> <xnat-project_id> mymaindirectory > output_log.txt
This script calls uploaddcmtk.sh so make sure you have both.