A Slicer extension to provide a GUI around pyradiomics
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JoostJM BUG: Revert Fix PyWavelets version to <= 1.0.0
Specifying the version in the no-binary part of the pip call breaks this argument, allowing slicer to install from the wheel. This in turn causes the DLL to fail to load, as a different compiler is used on Windows.
Revert the change here. The version is also fixed to <=1.0.0 in the PyRadiomics repository, and will therefore install the correct PyWavelets, including compiling it using Slicer's build setup.
Latest commit 4260d83 Dec 3, 2018

README.md

About

SlicerRadiomics is an extension for 3D Slicer that encapsulates pyradiomics library that calculates a variety of radiomics features.

See list and detailed description of computed features in pyradiomics library documentation.

Install instructions

SlicerRadiomics is currently distributed as an extension via the 3D Slicer ExtensionManager. Follow these steps to install the extension:

  1. Download the latest nightly release for your platform from http://download.slicer.org. Do NOT use installers tagged as "Stable Release"! If you use Mac, make sure you move the Slicer application to the Applications folder on your computer before launching it!
  2. Once installed, open Extension Manager by clicking the icon as shown below.
  3. Search for Radiomics and install the extension by clicking the INSTALL button.
  4. Once installation of Radiomics and dependencies is completed, you will need to restart Slicer application to access the module. If installation was successful, you should be able to see Radiomics module in the Slicer module list.

Building SlicerRadiomics from source

In order to build this extension, you need to have a version of Slicer built from source. You can build Slicer following the instructions. Once you have done that, all you need to do are the following steps:

  • Clone the source code of the repository.
$ git clone https://github.com/radiomics/SlicerRadiomics.git
  • Create an empty directory for building the extension.
$ mkdir SlicerRadiomics-build
  • Configure the build using cmake.
$ cd SlicerRadiomics-build
$ cmake -DSlicer_DIR:PATH=/path/to/Slicer-Release/Slicer-build ../SlicerRadiomics
  • Build the extension.
$ make

Note: cmake is one of the prerequisites for building 3D Slicer

Loading SlicerRadiomics from a build tree

There are two options:

Start Slicer specifying command-line options

  • Specify additonal launcher setting and module path.
cd SlicerRadiomics-build/inner-build/
build_dir=$pwd

./Slicer \
  --launcher-additional-settings $build_dir/AdditionalLauncherSettings.ini \
  --additional-module-path $build_dir
  • Open SlicerRadiomics module.

Package, install and restart Slicer

  • Package the extension.
$ cd inner-build
$ make package
  • Once completed, you can install the extension from file.

  • Restart Slicer and open SlicerRadiomics module.

Support

If you found a bug, or to report a reproducible problem, submit an issue.

If you have a question about using the extension, please ask on the mailing list.

Acknowledgments

This project is supported in part by the National Institutes of Health, National Cancer Institute Informatics Technology for Cancer Research (ITCR) program via grant U24 CA194354 (PI Hugo Aerts).