Multi Atlas Segmentation of brain anatomy using ANTs
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Multi Atlas Segmentation of Brain Anatomy: ANTs Example

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

A blog post explaininng Multi Atlas Segmentation:

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

git clone 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
cd Multi-Atlas-Segmentation

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