# Converting vtk to DICOM

**URL:** <https://discourse.slicer.org/t/converting-vtk-to-dicom/38041>\
**Category:** Support\
**Created:** [August 26, 2024, 9:22pm UTC](https://discourse.slicer.org/t/converting-vtk-to-dicom/38041 "2024-08-26T21:22:23Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![dbak](https://avatars.discourse-cdn.com/v4/letter/d/b19c9b/32.png) [@dbak](https://discourse.slicer.org/u/dbak)\
**Post date:** [August 26, 2024, 9:22pm UTC](https://discourse.slicer.org/t/converting-vtk-to-dicom/38041/1 "2024-08-26T21:22:23Z")

</div>

Hi! I have a VTK file (UnstructuredGrid) that I want to convert to a DICOM to share with my colleagues in medicine. I am familiar with VTKs but it is my first time doing anything with DICOM, so I would appreciate any help!

The VTK is of a 3D geometry and has a point data field (let’s call it P) that I want to project/show in the DICOM image.

I can import the VTK to Slicer as a Model and color it through “Scalars” by selecting the field P (see the top part of attached screenshot), but when I want to segment and turn it into a volume to later export as DICOM, I lose the coloring, and only the domain itself is colored by a single color (see lower part of screenshot)… I want to have the same coloring on the “slices” so I can have that as the DICOM…

Can anyone help me with this? Thank you very much!

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/5/e5bb1a74517e5b83534702079d1f375b27d5dd42.png)

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<div class="post-metadata">

**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [August 27, 2024, 9:19am UTC](https://discourse.slicer.org/t/converting-vtk-to-dicom/38041/2 "2024-08-27T09:19:20Z")

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I’m not aware of a really fitting format for this in DICOM. What I could imagine is to convert this “colored” mesh into a volume and export it as a conventional CT (or other image) modality. There is no module in Slicer to probe model into volume (only the other way around), but this function does this:

```auto
def probeMeshIntoVolume(self, inputMeshModel, currentMeshArrayName, inputVolume, outputVolume):
  """
  Probe values of a certain array at voxels of a reference volume and copy the probed values to an output volume.
  """
  # Get RAS to IJK transform of the input volume
  ras2IjkMatrix = vtk.vtkMatrix4x4()
  inputVolume.GetRASToIJKMatrix(ras2IjkMatrix)
  ras2IjkTransform = vtk.vtkTransform()
  ras2IjkTransform.SetMatrix(ras2IjkMatrix)
  # Apply the transformation to the grid
  transformFilter = vtk.vtkTransformFilter()
  transformFilter.SetInputData(inputMeshModel.GetUnstructuredGrid())
  transformFilter.SetTransform(ras2IjkTransform)
  transformFilter.Update()

  # Probe mesh with volume
  probeFilter = vtk.vtkProbeFilter()
  probeFilter.SetInputData(inputVolume.GetImageData())
  probeFilter.SetSourceData(transformFilter.GetOutputDataObject(0)) # The mesh grid transformed to IJK
  probeFilter.SetPassPointArrays(True) # Keep image points as scalars
  probeFilter.Update()

  # Create output volume from comparison
  outputVolume.SetRASToIJKMatrix(ras2IjkMatrix)
  outputVolume.SetName(f'Probed {inputMeshModel.GetName()} ({currentMeshArrayName}) with {inputVolume.GetName()}')
  outputShape = tuple(reversed(probeFilter.GetOutput().GetDimensions()))
  probeArray = vtk.util.numpy_support.vtk_to_numpy(probeFilter.GetOutput().GetPointData().GetArray(currentMeshArrayName))
  outputArray = probeArray.reshape(outputShape)
  slicer.util.updateVolumeFromArray(outputVolume, outputArray)

```

The only thing you need but don’t have is a reference volume. You can decide what resolution you need and either create a volume from scratch or load a sample volume and use it (after setting a different spacing if you want).

Then you can export the output volume into DICOM.  
[https://slicer.readthedocs.io/en/latest/developer\_guide/script\_repository.html#export-a-volume-to-dicom-file-format](https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#export-a-volume-to-dicom-file-format)