# Installing ITK Python package in Slicer 5.1 and above

**URL:** <https://discourse.slicer.org/t/installing-itk-python-package-in-slicer-5-1-and-above/25636>\
**Category:** Development\
**Tags:** python, itk, itk-python\
**Created:** [October 11, 2022, 5:12am UTC](https://discourse.slicer.org/t/installing-itk-python-package-in-slicer-5-1-and-above/25636 "2022-10-11T05:12:43Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [October 11, 2022, 5:12am UTC](https://discourse.slicer.org/t/installing-itk-python-package-in-slicer-5-1-and-above/25636/1 "2022-10-11T05:12:43Z")

</div>

Following the integration of Slicer pull request [#6564](https://github.com/Slicer/Slicer/pull/6564) adding support for ITK custom namespace, it is now possible to install ITK python package from PyPI and use associated filter.

The use of functionalities relying on either ITK C++ (e.g Slicer CLIs, vtkITK library, …) or the SimpleITK python package built within Slicer have been tested and are expected to work on macOS/Linux/Windows.

### Known Issues

- ITK pre-release ( `itk 5.3rc4.post3` or newer) should be used
- The use of macOS ITK python wheels is broken and issue is been discussed at [itk 5.3rc4.post3: Failure to load libtbb library (observed on macOS 10.13) - Engineering - ITK](https://discourse.itk.org/t/itk-5-3rc4-post3-failure-to-load-libtbb-library-observed-on-macos-10-13/5405)

### Installing the ITK Package

You may install the ITK python wheels using

```auto
slicer.util.pip_install(["--pre", "itk==5.3rc4.post3"])

```

_Alternatively, the instructions posted [here](https://github.com/Slicer/Slicer/pull/6564#issue-1396422082) allows to install the wheels in a dedicated directory. This more elaborated approach may be useful to avoid “polluting” the `site-packages` directory found in your installation of Slicer._

### Example: Applying ITK filter to MRML Volume node

The following example demonstrates how to apply an ITK filter to a MRML volume node:

```python
def updateMatrix3x3From4x4(matrix3x3, matrix4x4):
  for i_idx in range(3):
    for j_idx in range(3):
      matrix3x3.SetElement(i_idx, j_idx, matrix4x4.GetElement(i_idx, j_idx))

# Input node
import SampleData
input_volume_node = SampleData.SampleDataLogic().downloadMRHead()

# (1) Create VTK image data with expected metadata
input_vtk_image = vtk.vtkImageData()
input_vtk_image.ShallowCopy(input_volume_node.GetImageData())
input_vtk_image.SetOrigin(input_volume_node.GetOrigin())
input_vtk_image.SetSpacing(input_volume_node.GetSpacing())

directionMatrix4x4 = vtk.vtkMatrix4x4()
input_volume_node.GetIJKToRASDirectionMatrix(directionMatrix4x4)
directionMatrix3x3 = vtk.vtkMatrix3x3()
updateMatrix3x3From4x4(directionMatrix3x3, directionMatrix4x4)
input_vtk_image.SetDirectionMatrix(directionMatrix3x3)

# (2) Create ITK image data from VTK image data
import itk
input_itk_image = itk.image_from_vtk_image(input_vtk_image)

# (3) Filter ITK image
output_itk_image = itk.discrete_gaussian_image_filter(input_itk_image, variance=5.0)

# (4) Create output node
output_volume_node = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", "MRHead-Filtered")

# (5) Apply ITK filtering
vtk_output_image = itk.vtk_image_from_image(output_itk_image)

# (6) Update output node using on VTK output image spacing/origin/direction
ijkToRASMatrix = vtk.vtkMatrix4x4()
import vtkAddon
vtkAddon.vtkAddonMathUtilities.SetOrientationMatrix(vtk_output_image.GetDirectionMatrix(), ijkToRASMatrix)
output_volume_node.SetIJKToRASMatrix(ijkToRASMatrix)
output_volume_node.SetOrigin(*vtk_output_image.GetOrigin())
output_volume_node.SetSpacing(*vtk_output_image.GetSpacing())

# (7) Reset spacing/origin/direction from VTK output image
vtk_output_image.SetOrigin((0, 0, 0))
vtk_output_image.SetSpacing((1., 1., 1.))
identidyMatrix = vtk.vtkMatrix3x3()
vtk_output_image.SetDirectionMatrix(identidyMatrix)

# (8) Update output node setting VTK image data
output_volume_node.SetAndObserveImageData(vtk_output_image)

```

### Related posts

- [How to install ITK python wheels with Slicer 4.10 and Slicer 4.11?](https://discourse.slicer.org/t/how-to-install-itk-python-wheels-with-slicer-4-10-and-slicer-4-11/12537)

cc: @muratmaga @smrolfe @pranjal.sahu @thewtex

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<div class="post-metadata">

**Author:** ![smrolfe](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/smrolfe/32/3659_2.png) [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Post date:** [October 11, 2022, 5:30pm UTC](https://discourse.slicer.org/t/installing-itk-python-package-in-slicer-5-1-and-above/25636/2 "2022-10-11T17:30:05Z")

</div>

Thanks @jcfr, this is very exciting news! I think there may be a small typo above, to install I needed to change

> [@jcfr](#):
>
> `slicer.util.pip_install(["--pre", "itk==itk 5.3rc4.post3"])`

to

```auto
slicer.util.pip_install(["--pre", "itk==5.3rc4.post3"])

```

---

<div class="post-metadata">

**Author:** ![jcfr](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jcfr/32/17825_2.png) [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Post date:** [October 11, 2022, 5:59pm UTC](https://discourse.slicer.org/t/installing-itk-python-package-in-slicer-5-1-and-above/25636/3 "2022-10-11T17:59:33Z")

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> [@smrolfe](#):
>
> there may be a small typo above

Good catch 🙏 I edited the original post accordingly.