TubeTK hepatic vessel registration workflow

Algorithms
1

Hello all,

I recently read the Alward et al. paper on their unique way of registering blood vessels to DSAs. I’d like to implement it an ITK project and I found that group had created TubeTK. I’d like use TubeTK to register hepatic blood vessels to DSAs, but I can’t find an example of a workflow to follow. In other words, I’m not sure which of their ITK modules to use

2

Ping @Stephen_Aylward

3

@Stephen_Aylward
Good evening, I was hoping to use TubeTK to emulate the work that you did in your paper Registration and Analysis of Vascular Images, but I’m running into several problems. I tried following the instructions here to use TubeTK as a module of ITK. I have followed the instructions under the heading CompilingITKTubeTK: an ITK remote module!!!. I’m able to successfully compile and build ITK with TubeTK at this point.
My issue occurs here, when trying to accomplish the second portion of the task where it asks me to copy ITK’s and ITKTubeTK’s paths file into the site-packages directory. I’m having a problem with TubeTK’s path. I am unable to find the WrapITK.pth that is supposed to be in TubeTK’s directory. There is no Generators directory, or anything downstream of it.
I also noticed that in the wiki, it refers to ITKTubeTK as if it is built outside of the ITK build tree. But when I attempt to configure it, I receive the following cmake error:
CMake Error at C:/Users/henry/ITK/ITK-master/CMake/ITKModuleMacros.cmake:472 (add_library): add_library cannot create target "TubeTK" because an imported target with the same name already exists. Call Stack (most recent call first): src/CMakeLists.txt:37 (itk_module_add_library)
So I’m a little confused, as the first step is to build ITK with TubeTK enabled, but that blocks the ITKTubeTK out-of-source build later on.

4

Hi Henco,

You only need to compile ITK. You never need to checkout or compile TubeTK. I will try to make that clearer in the instructions.

When configuring ITK, simple set the following cmake variables:

  • CMAKE_BUILD_TYPE = Release
  • ITK_WRAP_PYTHON = On
  • Module_TubeTK = On

Also, if you don’t want to compile ITK, you can instead simply do

  • pip install itk-tubetk

Hope this helps, and I apologize for the out of date documentation.

s

1 Like
6

@Stephen_Aylward
Thank you for the help, I did manage to properly install TubeTK for use with python.
I still have a question regarding the framework you used to register a CT model to X-ray images in your group’s research paper “3D/2D Model-to-Image Registration Applied to TIPS Surgery”.
Is it possible to use TubeTK/src/Registration/itktubeImageToTubeRigidRegistration.h to register 3D/2D?