Difference between revisions of "Phenotyping"

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(Added Link to the documentation)
(Added build instructions)
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** [http://docs.mitk.org/nightly/classmitk_1_1GIFCooccurenceMatrix2.html Cooccurence matrix based features]
 
** [http://docs.mitk.org/nightly/classmitk_1_1GIFCooccurenceMatrix2.html Cooccurence matrix based features]
 
** [http://docs.mitk.org/nightly/classmitk_1_1GIFGreyLevelRunLength.html Run-length matrix based features]
 
** [http://docs.mitk.org/nightly/classmitk_1_1GIFGreyLevelRunLength.html Run-length matrix based features]
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== Building MITK Phenotyping from source ==
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# Install [https://www.qt.io/ Qt] on your system (>= 5.11.1).
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# Clone MITK from out [https://phabricator.mitk.org/source/mitk.git git repository] using [https://git-scm.com/ Git version control].
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# Configure the MITK Superbuild using [https://cmake.org/ CMake] (>= 3.10).
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## Choose the source code directory and an empty binary directory.
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## Click "Configure".
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## Check the option MITK_USE_SWIG.
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## Check the option MITK_USE_MatchPoint.
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## Click "Generate".
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# Build the project
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## Linux: Open a console window, navigate to the build folder and type "make -j8" (optionally supply the number threads to be used for a parallel build qith -j).
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## Windows (requires visual studio): Open the MITK Superbuild solution file and build all projects.
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# The build may take some time and should yield the binaries in "your_build_folder/MITK-build/bin"
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# After the build, open the "your_build_folder/MITK-build" folder in Cmake
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##
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## Check the option BUILD_BasicImageProcessingMiniApps
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## Check the option BUILD_ClassificationMiniApps
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## Check the option BUILD_org.mitk.gui.qt.radiomics
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## Check the option BUILD_org.mitk.gui.qt.multilabelsegmentation
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## Check the option BUILD_org.mitk.gui.qt.segmentation
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## Check the options BUILD_org.mitk.gui.qt.matchpoint.* depending on which elements you want in your view.
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More detailed build instructions can be found in the [http://docs.mitk.org/nightly/BuildInstructionsPage.html documentation.]

Revision as of 15:03, 5 October 2018

MITK Phenotyping is a selection of different methods and algorithms that can be used for Radiomics-related research and application building. It is mainly developed within the Division Medical Image Computing at the German Cancer Research Center (DKFZ).

MITK Phenotyping is part of the main MITK Software. Currently, it contains some software part that are not yet integrated in the main release. It is planned to merge both, MITK Phenotyping and MITK Workbench into a single software package.

Features & Highlights

Support for most established medical imaging file formats

  • Images: DICOM, NIFTI, NRRD and other
  • VTK file formats (for meshed, point sets etc..)

Image preprocessing

  • Registration using MatchPoint
  • Image Filtering and processing
    • Laplacian of Gaussian (LoG)
    • Wavelet-Transformation
    • Mathematical Operations

Semiautomatic Segmentation

  • Multilabel Support
  • Several manual and semiautomatic segmentation methods
  • Extra Tools for Segmentation Cleaning / Postprocessing

Radiomics Feature Calculation

  • Wide range of possible Features
  • Tested in combination with the IBSI initiative
  • Possibility of encoding feature parameters in feature names


Documentation and Help

The modules and Tools are documented within the MITK documentation. The following list directly lists the most importants parts of this documentation:


Building MITK Phenotyping from source

  1. Install Qt on your system (>= 5.11.1).
  2. Clone MITK from out git repository using Git version control.
  3. Configure the MITK Superbuild using CMake (>= 3.10).
    1. Choose the source code directory and an empty binary directory.
    2. Click "Configure".
    3. Check the option MITK_USE_SWIG.
    4. Check the option MITK_USE_MatchPoint.
    5. Click "Generate".
  4. Build the project
    1. Linux: Open a console window, navigate to the build folder and type "make -j8" (optionally supply the number threads to be used for a parallel build qith -j).
    2. Windows (requires visual studio): Open the MITK Superbuild solution file and build all projects.
  5. The build may take some time and should yield the binaries in "your_build_folder/MITK-build/bin"
  6. After the build, open the "your_build_folder/MITK-build" folder in Cmake
    2. Check the option BUILD_BasicImageProcessingMiniApps
    3. Check the option BUILD_ClassificationMiniApps
    4. Check the option BUILD_org.mitk.gui.qt.radiomics
    5. Check the option BUILD_org.mitk.gui.qt.multilabelsegmentation
    6. Check the option BUILD_org.mitk.gui.qt.segmentation
    7. Check the options BUILD_org.mitk.gui.qt.matchpoint.* depending on which elements you want in your view.

More detailed build instructions can be found in the documentation.

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