JanaLipkova/Registration

Image registration using ANTs

Image Registrations Using ANTs Library

This code provides simple scripts for image registrations using ANTs library, together with examples.

References: Jana Lipkova (jana.lipkova@tum.de)

1) Install ANTs

git clone git://github.com/stnava/ANTs.git
mkdir antsbin
cd antsbin
ccmake ../ANTs
make -j 4

Set the path to the installed library by updating your ~/.profile or ~/.basrc file with the following lines, where the first line contains path to YOUR library:

export ANTSPATH=/home/jana/Work/Ants/stnava-ANTs-a430c38/antsbin/bin/
export PATH=$PATH:$ANTSPATH

For more installaiton info see: http://sourceforge.net/projects/advants/files/ANTS/ANTS_Latest/

2) Registrations scripts

Folder source contains scripts for registration:

• scripts with word Registration in the name perfom specific registration (for now only non-deformable registrations scripts, i.e. registrations that transform the whole image). The transformation matrix is stored as output in the .mat file
• scripts with word Transformation apply existing transformation from the mat file on the specified images

Syntax of the scripts:

./affineRegistrations.sh moving_image.nii fixed_image.nii output_image.nii
./applyTransformation.sh moving_image.nii fixed_image.nii output_image.nii transformationMatrix.mat

3) Example

Folder example contains three nifty files.

1. We will first register atlas.nii to t1.nii with i.e. affine registration do:

./affineRegistration.sh atlas.nii t1.nii atlas2t1.nii

2. It will create also mat file with corresponding transformation. The transformation mask can be used to map the atlas brain mask atlas_mask.nii into the t1.nii:

./applyTransformation.sh atlas_mask.nii t1.nii mask2t1.nii atlas2t1.nii0GenericAffine.mat

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