irAEMM

Immunotherapy related adverse effects toolbox

Manage images and data related to irAE project.

Slicer module

Installation

Download the code and dependencies. Unzip. To have Slicer know where the files are, open Slicer, and under Edit->Application settings select Modules section. Under Paths, click on Add and navigate to newly unzipped directories. We need labkeyBrowser and DICOMtools from SlcierLabkeyExtension and slicerModule from iraeMM code. After clicking OK, Slicer will and has to be restarted.

Setup

To access LabKey, the Slicer tools must be configured. Do that by selecting LabKey->labkeyBrowser module from module list and fill appropriate fields.

Onko-nix

For accessing OIL internal site, the settings are:

• Server: `http://onko-nix.onko-i.si:8080
• Labkey username: username, given at the LabKey site, typically your email
• Labkey password: password, generated when accessing LabKey site

Dependencies

To access LabKey, the python API was used. Anonymization and NIfTI conversion are based on phenomenal nibabel tools. Data storage is provided by Orthanc with associated interface.

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.