Merge branch 'master' of wiscigt.powertheword.com:andrej.studen/iraemm

README.md

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+# Immunotherapy related adverse effects toolbox
+
+Manage images and data related to irAE project.
+
+### Dependencies 
+To access LabKey, the [python API][labkeyInterface] was used.
+Anonymization and NIfTI conversion are based on phenomenal [nibabel][] tools. 
+Data storage is provided by [Orthanc][] with associated [interface][orthancInterface].
+
+### Usage
+
+Anonymization must be run as a `tomcat8` user for access to data files. Check setup 
+in the `anonymization.py` and run it with `runPython.sh anonymization.py`. 
+
+
+[nibabel]: https://nipy.org/nibabel/gettingstarted.html
+[labkeyInterface]: http://wiscigt.powertheword.com/andrej.studen/labkeyInterface
+[Orthanc]:https://www.orthanc-server.com
+[orthancInterface]: http://wiscigt.powertheword.com/andrej.studen/orthancinterface