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.
See License.txt
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
Find the tool on NITRC