Applying Affine matrix to new image

I have used a program to register images and have it out put the affine matrix used to align the images. I would now like to make a program that can apply that same matrix to other images without having to go through the whole registration process again. I am currently using the imwarp command and am referencing two reference objects. However, my image is being output of the imwarp command as a different size then the input. I am currently using the same image that I registered originally to confirm that applying the matrix alone works as well. Any suggestions?

[Matthew Krispin]

It’s an issue of the size of image and scaling. I am able to see that the shape in the image is the correct shape but placed incorrectly within the image field and scaled incorrectly. Is this an issue of the affine parameters?