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extract 2D slice (defined by arbitrary plane intersection) from 3D volume using either iTK or scipy ndimage and interpolation with SimpleITK. Does anyone have a working example ? I have read several posts here and on the ITK users list but no one has a something that works. Thanks

GT

user1301295
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  • How are you defining your plane? How are your defining your image domain? – blowekamp Jan 11 '18 at 18:03
  • the image is read with simpleitk like so: itkimage = sitk.ReadImage(mhd_file) , for the bounds one can get easily 0*itkimage.GetSpacing()[0] + itkimage.GetOrigin()[0], (itkimage.GetWidth()-1)*itkimage.GetSpacing()[0] + itkimage.GetOrigin()[0], for the plane, I am using a normal [n1,n2,n3] and two vectors, u, and v which orthogonal to the normal. thanks – user1301295 Jan 11 '18 at 22:49
  • So you have a good orthonormal basis. Are these vector is the physical space domain or the pixel space domain? or Some other? It would be easiest if is was Physical space. With this information you system is still under determined, you also need a point which the plane is passing through. – blowekamp Jan 12 '18 at 15:07
  • These are all defined in physical space and I have one point on the plane. Do you have a pseudocode or snippet ? Thanks //GT – user1301295 Jan 31 '18 at 21:37

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