This repo has script and data for multi atlas segmentation of brain anatomy with ANTs package.

A blog post explaininng Multi Atlas Segmentation: http://blog.qure.ai/notes/brain-anatomy-segmentation

To run the script, you need to install ANTs. Follow these instructions to build ANTs from source:

git clone git://github.com/stnava/ANTs.git
mkdir ANTs/bin
cd ANTs/bin
cmake ..
make -j 4 # This might take a while

cp ../Scripts/* bin
# Mac users change bashrc to bash_profile
echo export ANTSPATH=`pwd`/bin/ >> ~/.bashrc 
source ~/.bashrc

Once ANTs is installed, run the following commands:

git clone https://github.com/qureai/Multi-Atlas-Segmentation.git
cd Multi-Atlas-Segmentation
bash multi-atlas-segmentation.sh

This will create a file predictions/1004_predLabels.nii.gz containing predicted labels of test image.

Training and test images are from MICCAI12 grand challenge on Multi-Atlas Labeling