XNAT Tips and Tricks

Users familiar with command line can automate downloads and some analysis of data on XNAT via PyXNAT: https://pythonhosted.org/pyxnat/

The PyXNAT page has a tutorial located here: https://pythonhosted.org/pyxnat/tutorial.html 

Users on TACC can access XNAT directly using setup_subject.

Run:

module use /work/IRC/opt/modules

module load irc_python

module load setup_subject

Create a directory to work under, for example I might do:

cd $WORK

mkdir mystudy

then by calling setup_subject like this:

setup_subject.py --xnat-project <your project ID> --getdata --keepdata -b . --studyname mystudy -s <your subject's id>

This will access and download your scans automatically.