Hi,
I'm using CMTK on Windows (via the Cygwin terminal) to register image stacks of zebrafish brains to a reference atlas. The registration to the atlas works very well. After registration, I use the transformation data to apply the inverse transformation to binary masks originally defined in atlas space, in order to bring them into the native space of each sample (each sample has its own transformation, so that each output mask is aligned to the corresponding brain).

However, I’m encountering problems during this inverse transformation step. When I apply the inverse transformation using the following command:

C:/cygwin64/usr/local/lib/cmtk/bin/reformatx -v -o zf1_tectum.nrrd
--floating D:/Atlas_registration/Reg_folder/images/tectum.nrrd D:/Atlas_registration/Reg_folder/images/zf1_01.nrrd
--inverse D:/Atlas_registration/Reg_folder/Registration/warp/Kunst_zf1_01_warp_m0g80c8e1e-1x52r3.list/registration/registration

the resulting mask is not properly aligned to the sample brain.

First, the orientation of the mask appears to be rotated by 180° compared to the sample (attached image, left). If I manually correct the rotation using ImageJ, I still observe a significant mismatch between the position of the mask and its expected location in the brain (attached image, right). Specifically, there seems to be a translation issue in the XY plane, while the Z position looks approximately correct.

What could be the cause of this misalignment?
Is there a way to avoid it?

Thanks in advance for any help or suggestions.