About affine transformation

[taipingqu]

Dear expert, how do I use ANTs to do affine alignment based on my own template? Could you tell me the command?

[ntustison]

You can use antsRegistrationSyNQuick.sh. To get the help menu, use

$ antsRegistrationSyNQuick.sh -h 1

For an affine transform, you could do something like

$ antsRegistrationSyNQuick.sh -d 3 -t a -f ${fixedImage} -m ${movingImage} -o ${outputPrefix}

[taipingqu]

Hi,I use the command you gave above to do affine alignment, how to output affine.txt?

[cookpa]

We use the .mat format for affine transforms now. This will be produced by the antsRegistrationSyNQuick.sh.

antsRegistrationSyNQuick.sh -d 3 -t a -f ${fixedImage} -m ${movingImage} -o ${outputPrefix}

antsApplyTransforms -d 3 -r ${fixedImage} -i ${movingImage} -t ${outputPrefix}0GenericAffine.mat

https://github.com/ANTsX/ANTs/wiki/Forward-and-inverse-warps-for-warping-images,-pointsets-and-Jacobians