chicken

a global optimization example + landmark distances performed with ITK and ANTs

Global optimization. You may need to change the parameters for your own application.

See the code here which uses ITK multi-start optimization

antsAffineInitializer 2 chicken-4.jpg chicken-3.jpg chicken3to4.mat 10 0.3 0 10

Now apply the results to warp the images and the labels.

antsApplyTransforms -d 2 -i chicken-3.jpg -o test.nii.gz -r chicken-4.jpg -t chicken3to4.mat antsApplyTransforms -d 2 -i chicken-3-seg.nii.gz -o chicken-3-segw.nii.gz -r chicken-4.jpg -t chicken3to4.mat -n NearestNeighbor

Now convert to csv files to take a look at point-wise results.

ImageMath 2 chicken-3.csv LabelStats chicken-3-seg.nii.gz chicken-3-seg.nii.gz ImageMath 2 chicken-3w.csv LabelStats chicken-3-segw.nii.gz chicken-3-segw.nii.gz

Transform the points.

antsApplyTransformsToPoints -d 2 -i chicken-3.csv -o test.csv -t [chicken3to4.mat ,1 ]

And compare - test.csv should be similar to chicken-3w.csv ...

The example images are here: