For how to replace the function GetPixelValueByIndex see:
http://docs.mitk.org/2013.06/deprecatedSince2012_09.html
Affected classes:
Core/Code/Controllers/mitkSliceNavigationController.cpp
Core/Code/DataManagement/mitkImage.cpp
Core/Code/DataManagement/mitkImage.h
Core/Code/Testing/mitkExtractSliceFilterTest.cpp
Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkCreator.cpp
Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImporter.cpp
Modules/Python/Testing/mitkCopyToPythonAsItkImageTest.cpp
Modules/Qmitk/QmitkStdMultiWidget.cpp
Modules/QmitkExt/QmitkAdaptiveRegionGrowingWidget.cpp
Modules/QmitkExt/QmitkVtkLineProfileWidget.cpp
Modules/Segmentation/Testing/mitkOverwriteSliceFilterObliquePlaneTest.cpp
Modules/Segmentation/Testing/mitkOverwriteSliceFilterTest.cpp
Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp
Modules/ToFProcessing/Testing/mitkToFCompositeFilterTest.cpp
Modules/ToFProcessing/Testing/mitkToFDistanceImageToPointSetFilterTest.cpp
Modules/ToFProcessing/Testing/mitkToFDistanceImageToSurfaceFilterTest.cpp
Modules/ToFProcessing/mitkToFDistanceImageToPointSetFilter.cpp
Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTbssSkeletonizationView.cpp
Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkBooleanOperationsView.cpp