Hi Miri,
you need to apply the geometry of your image to the surface so that both have
the same origin. The code for doing that looks like the following:
TimeSlicedGeometry::Pointer originalGeometry;
AffineGeometryFrame3D::Pointer originalGeometryAGF =
mitk_Image->GetTimeSlicedGeometry()->Clone();
originalGeometry = dynamic_cast<TimeSlicedGeometry*>(
originalGeometryAGF.GetPointer() );
//Since the surface is no image geometry and hence should not be shifted
for 0.5
originalGeometry->ChangeImageGeometryConsideringOriginOffset(false);
outputSurface->SetGeometry( originalGeometry );
Regards
Andreas
On 14.12.2011, at 16:30, Miri Trope wrote:
Hi All,
My algorithm has just generated a wonderful scalp extraction from T1 MRI image.
Now, I'm dealing with an irritating problem: that surface has been shifted as
seen in the attachment.
How can I overcome that?
Flow chart of my conversions:
itk_Image => mitk_Image => vtk_Image => vtkPolyData
Snap code:
//some manipulations on itk image
mitk::CastToMitkImage(itk_Image, mitk_Image);
vtkImageData* vtkImage = vtkImageData::New();
vtk_Image = mitk_Image->GetVtkImageData();
// smoothing
vtkImageGaussianSmooth* smooth = vtkImageGaussianSmooth::New();
vtkImageMedian3D* med = vtkImageMedian3D::New();
smooth->SetInput(vtkImage);
med->SetInput(smooth->GetOutput());
med->SetKernelSize(3,3,2);
// conversion to vtk poly data
vtkContourFilter* image2poly = vtkContourFilter::New();
image2poly->SetInput ( (vtkDataSet*)med->GetOutput());
image2poly->SetValue(0,1);
// pick the largest component
vtkPolyDataConnectivityFilter* connectivity =
vtkPolyDataConnectivityFilter::New();
connectivity->ScalarConnectivityOff();
connectivity->SetExtractionModeToLargestRegion();
connectivity->SetInput(image2poly->GetOutput());
// in order to view my output surface on mitk gui
mitk::Surface::Pointer outputSurface::Surface::New();
outputSurface->SetVtkPolyData(connectivity->GetOutput());
outputSurface->Update();
vtkPolyDataWriter* writerPD = vtkPolyDataWriter::New();
writerPD->SetInput(connectivity->GetOutput());
writerPD->SetFileName("Surface.vtk");
writerPD->SetFileTypeToASCII();
writerPD->Write();
<surface.JPG>------------------------------------------------------------------------------
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