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3D Slicer Extension for PETTumorSegmentation

License: Other

C++ 71.87% CMake 2.99% Python 25.14%

nci-qin 3d-slicer-extension 3d-slicer

pettumorsegmentation's Introduction

PETTumorSegmentation

Slicer Extension for tumor and lymph node segmentation in PET scans

Documentation: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETTumorSegmentation

This work is funded in part by Quantitative Imaging to Assess Response in Cancer Therapy Trials NIH grant U01-CA140206 (PIs John Buatti, Tom Casavant, Michael Graham, Milan Sonka), Quantitative Image Informatics for Cancer Research (QIICR) NIH grant U24 CA180918, and Graph-based Medical Image Segmentation in 3D and 4D NIH grant R01 EB004640

pettumorsegmentation's People

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jcfr che85 fedorov lunarplugins pieper jianglimed devhliu claudiasconstantino yolanda1993 khangthk

pettumorsegmentation's Issues

Extension not working

When I click in a tumour the extension is not creating segments

slicer.qSlicerSeg... effects are not accessible when installing this extension

Basically effects are normally accessible from the python console. The following should be displayed when using auto completion (which is not the case after installing PETTumorSegmentation):

Tool does not work right in LongitudinalPETCT

When this effect is used in the embedded EditorWidget of LongitudinalPETCT the undo/redo functionality is not working correctly.

One issue that the code accesses the Editor module widget which may not exist if the Editor module has not been entered, and in any case the variable would not be associated with the buttons in the embedded widget.

Since the effect tool is passed in the Editor's instance of the UndoRedo class it should be possible to implement the save and restore state functionality without accessing the widget.

Using effect and then selecting SegmentEditor "No editing" cursor hides cursor from slice widgets

There is no cursor visible after using this effect

Extension not available on Mac as of Jun 7, 2016

There appear to be build errors on mac

http://slicer.cdash.org/viewBuildError.php?buildid=840788

can i use this code to segment knee cartilage?

Recently I read many Prof. Milan Sonka's papers and I am really interested in LOGISMOS.
But I did not find the source of LOGISMOS.
I wonder if I can reproduce LOGISMOS according to this code
My English is not very good, please forgive me if I speak stiffly

I can't find this extension in the 3d slicer

I can't find this plugin in 3dslicer 4.10.1 according to the tutorial in Wikipedia. Was it deleted？

Build error on linux

http://slicer.cdash.org/buildSummary.php?buildid=1184598

make[5]: *** No rule to make target `/home/kitware/Dashboards/Nightly/Slicer-0-build/Slicer-build/lib/Slicer-4.9/qt-loadable-modules/libvtkSlicerSegmentationsModuleLogic.so', 
needed by `lib/Slicer-4.9/qt-loadable-modules/libvtkSlicerPETTumorSegmentationModuleMRML.so'.  Stop.

cc: @cpinter

Creation of master-4.10 branch

To streamline the development, I suggest to create a branch based of 0e45ef9 and then update https://github.com/Slicer/ExtensionsIndex/blob/4.10/PETTumorSegmentation.s4ext to reference master-4.10.

Doing so will allow to fix build issue associated with the transition to ITKv5 and avoid to manage complex #if/#else.

Fix narrowing warnings

Building against Slicer r24904 on Ubuntu 15.10 using g++ 5.2.1 returns the following

/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx: In member function ‘itk::Image<short int, 3u>::Pointer vtkSlicerPETTumorSegmentationLogic::ConvertLabelImageToITK(vtkMRMLPETTumorSegmentationParametersNode*, vtkImageData*)’:
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:189:119: warning: narrowing conversion of ‘-(* vtkLabelVolume->vtkMRMLScalarVolumeNode::<anonymous>.vtkMRMLVolumeNode::GetOrigin())’ from ‘double’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
   float origin2[3] = {-vtkLabelVolume->GetOrigin()[0], -vtkLabelVolume->GetOrigin()[1], vtkLabelVolume->GetOrigin()[2]};
                                                                                                                       ^
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:189:119: warning: narrowing conversion of ‘-(*(vtkLabelVolume->vtkMRMLScalarVolumeNode::<anonymous>.vtkMRMLVolumeNode::GetOrigin() + 8u))’ from ‘double’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:189:118: warning: narrowing conversion of ‘*(vtkLabelVolume->vtkMRMLScalarVolumeNode::<anonymous>.vtkMRMLVolumeNode::GetOrigin() + 16u)’ from ‘double’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
   float origin2[3] = {-vtkLabelVolume->GetOrigin()[0], -vtkLabelVolume->GetOrigin()[1], vtkLabelVolume->GetOrigin()[2]};
                                                                                                                      ^
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx: In member function ‘itk::Image<float, 3u>::Pointer vtkSlicerPETTumorSegmentationLogic::GetPETVolume(vtkMRMLPETTumorSegmentationParametersNode*)’:
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1765:113: warning: narrowing conversion of ‘-(* vtkPetVolume->vtkMRMLScalarVolumeNode::<anonymous>.vtkMRMLVolumeNode::GetOrigin())’ from ‘double’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
   float origin2[3] = {-vtkPetVolume->GetOrigin()[0], -vtkPetVolume->GetOrigin()[1], vtkPetVolume->GetOrigin()[2]};
                                                                                                                 ^
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1765:113: warning: narrowing conversion of ‘-(*(vtkPetVolume->vtkMRMLScalarVolumeNode::<anonymous>.vtkMRMLVolumeNode::GetOrigin() + 8u))’ from ‘double’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1765:112: warning: narrowing conversion of ‘*(vtkPetVolume->vtkMRMLScalarVolumeNode::<anonymous>.vtkMRMLVolumeNode::GetOrigin() + 16u)’ from ‘double’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
   float origin2[3] = {-vtkPetVolume->GetOrigin()[0], -vtkPetVolume->GetOrigin()[1], vtkPetVolume->GetOrigin()[2]};
                                                                                                                ^
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx: In instantiation of ‘typename ITKImageType::Pointer vtkSlicerPETTumorSegmentationLogic::convert2ITK(vtkSmartPointer<vtkImageData>) [with ITKImageType = itk::Image<short int, 3u>; typename ITKImageType::Pointer = itk::SmartPointer<itk::Image<short int, 3u> >]’:
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:187:85:   required from here
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1583:103: warning: narrowing conversion of ‘-(&(& itkVolume.itk::SmartPointer<TObjectType>::operator-><itk::Image<short int, 3u> >()->itk::Image<short int, 3u>::<anonymous>)->itk::ImageBase<VImageDimension>::GetOrigin<3u>())->itk::Point<double, 3u>::<anonymous>.itk::FixedArray<TValue, VLength>::operator[]<double, 3u>(0)’ from ‘itk::FixedArray<double, 3u>::ValueType {aka double}’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
   float origin[3] = {-itkVolume->GetOrigin()[0], -itkVolume->GetOrigin()[1], itkVolume->GetOrigin()[2]};
                                                                                                       ^
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1583:103: warning: narrowing conversion of ‘-(&(& itkVolume.itk::SmartPointer<TObjectType>::operator-><itk::Image<short int, 3u> >()->itk::Image<short int, 3u>::<anonymous>)->itk::ImageBase<VImageDimension>::GetOrigin<3u>())->itk::Point<double, 3u>::<anonymous>.itk::FixedArray<TValue, VLength>::operator[]<double, 3u>(1)’ from ‘itk::FixedArray<double, 3u>::ValueType {aka double}’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1583:103: warning: narrowing conversion of ‘(itk::FixedArray<double, 3u>::ValueType)(&(& itkVolume.itk::SmartPointer<TObjectType>::operator-><itk::Image<short int, 3u> >()->itk::Image<short int, 3u>::<anonymous>)->itk::ImageBase<VImageDimension>::GetOrigin<3u>())->itk::Point<double, 3u>::<anonymous>.itk::FixedArray<TValue, VLength>::operator[]<double, 3u>(2)’ from ‘itk::FixedArray<double, 3u>::ValueType {aka double}’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx: In instantiation of ‘typename ITKImageType::Pointer vtkSlicerPETTumorSegmentationLogic::convert2ITK(vtkSmartPointer<vtkImageData>) [with ITKImageType = itk::Image<float, 3u>; typename ITKImageType::Pointer = itk::SmartPointer<itk::Image<float, 3u> >]’:
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1763:74:   required from here
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1583:103: warning: narrowing conversion of ‘-(&(& itkVolume.itk::SmartPointer<TObjectType>::operator-><itk::Image<float, 3u> >()->itk::Image<float, 3u>::<anonymous>)->itk::ImageBase<VImageDimension>::GetOrigin<3u>())->itk::Point<double, 3u>::<anonymous>.itk::FixedArray<TValue, VLength>::operator[]<double, 3u>(0)’ from ‘itk::FixedArray<double, 3u>::ValueType {aka double}’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1583:103: warning: narrowing conversion of ‘-(&(& itkVolume.itk::SmartPointer<TObjectType>::operator-><itk::Image<float, 3u> >()->itk::Image<float, 3u>::<anonymous>)->itk::ImageBase<VImageDimension>::GetOrigin<3u>())->itk::Point<double, 3u>::<anonymous>.itk::FixedArray<TValue, VLength>::operator[]<double, 3u>(1)’ from ‘itk::FixedArray<double, 3u>::ValueType {aka double}’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]
/home/jcfr/Projects/PETTumorSegmentation/PETTumorSegmentation/Logic/vtkSlicerPETTumorSegmentationLogic.cxx:1583:103: warning: narrowing conversion of ‘(itk::FixedArray<double, 3u>::ValueType)(&(& itkVolume.itk::SmartPointer<TObjectType>::operator-><itk::Image<float, 3u> >()->itk::Image<float, 3u>::<anonymous>)->itk::ImageBase<VImageDimension>::GetOrigin<3u>())->itk::Point<double, 3u>::<anonymous>.itk::FixedArray<TValue, VLength>::operator[]<double, 3u>(2)’ from ‘itk::FixedArray<double, 3u>::ValueType {aka double}’ to ‘float’ inside { } is ill-formed in C++11 [-Wnarrowing]

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