How to work with .mha + .raw files

Beginner Questions
1

Hi,

I am trying to see how to read data sets of lets say a ct scan (e.g. sinogram): following are my concerns:

  1. how to get the data set of projections. any public site or university site
  2. how to use ITK VTK to reconstruct the images into a volume
  3. do some segmentations on different slices, lets say I have 64 slices of a ct scan.
  4. I want to segment it and then reconstruct it with Filter Back Projection or ART or ML-EM or OSEM or combinations of all the above!
  5. are these reconstruction techniques in ITK or VTK or a combination of both

I hope to get the sonograms of 0-180 degrees for lets say 64 slices

thanks in advance for any help

Regards,
sag

2

Hi sag,

Please take a look at the ITK-based Reconstruction Toolkit (RTK) – this has much of the desired functionality.

Regards,
Matt

@simon.rit

1 Like
3

Hi matt,

Firstly thank you for the help!

  1. I did download the RTK, then I separately from ITK tried to build the RTK source code but failed with different configuration errors in CMake before generate and build it in vs2017 just like I did with VTK & ITK. Then I saw article that I should copy it to the Modules folder of ITK and build and install them together! this worked but when I tried to test my installation with HelloWorld of RTK it gives error in configure in CMake that RTK is not installed!? technically RTK is all under ITK and there is no path for RTK in my system path!

  2. This is HelloWorld/CMakeList.txt file:

cmake_minimum_required(VERSION 2.8)
project(HelloWorld)

if(NOT TARGET RTK)
   find_package(RTK REQUIRED)
   include(${RTK_USE_FILE})
endif

add_executable(HelloWorld    HelloWorld.cxx)
target_link_libraries(HelloWorld ${RTK_LIBRARIES})
target_link_libraries(HelloWorld ${ITK_LIBRARIES})

can I set the path for RTK which is nested inside the ITK with set or set path inside this HelloWorld/CMakeLists.txt file so the build process can go and find RTK build inside the ITK build which is on my system path of PC?

  1. How do you install RTK separately from ITK without getting stuck in CMake configure step?

Regards
sag

4

Discussion continued in a new thread: RTK installation problem any help appreciated.