Brain segmentation on .VTK head surface

Web
4

Hey Julien,
I’m sorry for the late ressponse, sorry I didn’t want to say “by segmentation” the real segmentation that we use in the medical field, It’s just a reshaping of the VTK surface to be identic to the VTI volume at a certain depth, like the video there,
ezgif-1-144f08ef9f

For the pipeline (C++) to do so:

  • We charge a .nii MRI and a Skin VTK (a human head)
  • We get the bounds (bounds[6]) from the nii reader.
  • We calculate sizes:
    xSize = bounds[1] - bounds[0];
    ySize = bounds[3] - bounds[2];
    zSize = bounds[5] - bounds[4];
  • We create a vtkPlane that we set its Origin values to Sizes
    vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
    plane->SetOrigin(xSize/2.0,ySize/2.0,zSize/2.0);
    plane->SetNormal(0.0, 0.0, 1.0);
  • We create a vtkDecimatePro that we set Input Connection to the Output of skin VTK reader
  vtkSmartPointer<vtkDecimatePro> deci=vtkSmartPointer<vtkDecimatePro>::New();
  deci->SetInputConnection(vtkReader->GetOutputPort());
  deci->SetTargetReduction(0.6);
  deci->PreserveTopologyOn();
  • We create a vtkSmoothPolyDataFilter that we set its Input Connection to vtkDecimatePro Outport
    vtkSmartPointer
  smoother=vtkSmartPointer<vtkSmoothPolyDataFilter>::New();
  smoother->SetInputConnection(deci->GetOutputPort());
  smoother->SetRelaxationFactor(0.8);
  smoother->SetNumberOfIterations(100);
  smoother->BoundarySmoothingOff();
  smoother->FeatureEdgeSmoothingOff();
  • We create a vtkTransform that we set its Translate to Sizes/2
  vtkSmartPointer<vtkTransform> transform = vtkSmartPointer<vtkTransform>::New();
  transform->Identity();
  transform->PostMultiply();
  transform->Translate(xSize/2.0,ySize/2.0,zSize/2.0);
  transform->Scale(1,1,1);
  transform->Translate(xSize/2.0,ySize/2.0,zSize/2.0);
  • We create vtkTransformPolyDataFilter that we set its Input Connection to vtkSmoothPolyDataFilter and its Transform to vtkTransform:
  vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
  transformFilter->SetInputConnection(smoother->GetOutputPort());
  transformFilter->SetTransform(transform);
  transformFilter->Update();
  • Here where we use vtkProbeFilter :
  vtkSmartPointer<vtkProbeFilter> probe = vtkSmartPointer<vtkProbeFilter>::New();
  probe->SetInputConnection(transformFilter->GetOutputPort());
  probe->SetSourceData(niiReader->GetOutput());
  probe->SpatialMatchOn();
  probe->Update();
  vtkSmartPointer<vtkPolyDataMapper> map = vtkSmartPointer<vtkPolyDataMapper>::New();
  map->SetInputConnection(probe->GetOutputPort());
  map->SetScalarRange(probe->GetOutput()->GetScalarRange());
  vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
  actor->SetMapper(map);
1 Like