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@@ -5,7 +5,24 @@ Manage images and data related to irAE project.
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# Slicer module
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## Installation
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-Download the [code][iraemm] and [dependencies][]
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+Download the [code][iraemm] and [dependencies][SlicerLabkeyExtension]. Unzip. To
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+have Slicer know where the files are, open Slicer, and under Edit->Application settings
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+select Modules section. Under Paths, click on Add and navigate to newly unzipped
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+directories. We need `labkeyBrowser` and `DICOMtools` from `SlcierLabkeyExtension` and
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+`slicerModule` from `iraeMM` code. After clicking `OK`, Slicer will and has to
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+be restarted.
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+
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+## Setup
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+To access LabKey, the Slicer tools must be configured. Do that by selecting LabKey->labkeyBrowser
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+module from module list and fill appropriate fields.
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+
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+### Onko-nix
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+For accessing OIL internal site, the settings are:
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+- Server: `http://onko-nix.onko-i.si:8080
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+- Labkey username: username, given at the LabKey site, typically your email
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+- Labkey password: password, generated when accessing LabKey site
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+
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+
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### Dependencies
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@@ -18,7 +35,7 @@ Data storage is provided by [Orthanc][] with associated [interface][orthancInter
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Anonymization must be run as a `tomcat8` user for access to data files. Check setup
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in the `anonymization.py` and run it with `runPython.sh anonymization.py`.
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-
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+[SlicerLabkeyExtension]:http://wiscigt.powertheword.com/labkey/SlicerLabkeyExtension/-/archive/SlicerExtensionIndex/SlicerLabkeyExtension-SlicerExtensionIndex.zip
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[iraemm]: http://wiscigt.powertheword.com/oil/iraemm/-/archive/master/iraemm-master.zip
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[nibabel]: https://nipy.org/nibabel/gettingstarted.html
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[labkeyInterface]: http://wiscigt.powertheword.com/andrej.studen/labkeyInterface
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