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NeoSegPipeline/MultiSegPipeline

What is it?

This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates an subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then we run a single atlas method with this atlas and obtain some good results, especially for in subcortical midbrain structure. We also included a tool to average deformation fields.

License

See License.txt

Build instructions

It builds the software tool and all the dependencies. If you want to build ANTs, check the option `BUILD_ANTs' in the cmake menu.

  git clone https://github.com/NIRALUser/NeosegPipeline.git
  mkdir NeosegPipeline-build
  cd NeosegPipeline-build
  cmake ../NeosegPipeline
  make

If you run into build issues if it does not find the Qt5 libs, then go into the MultisegPipeline build subdirectory and run ccmake there to provide the Qt5_Dir and finally run make

  cd MultisegPipeline-build
  ccmake ../../NeosegPipeline/
  make

More information

Find the tool on NITRC