I think Sandor is right that you might not want to refer to :
Kunst_zf1_01_warp_m0g80c8e1e-1x52r3.list/registration/registration
In your command but instead just
Kunst_zf1_01_warp_m0g80c8e1e-1x52r3.list
I’m guessing that there was a gzip compressed file like this:
Kunst_zf1_01_warp_m0g80c8e1e-1x52r3.list/registration.gz
and at some point this got expanded making a new registration subfolder with a registration file inside. However I don’t know if that could actually be your problem.
Otherwise I don’t notice anything unusual about your 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
I would potentially check the headers of your different files. If you have unu installed you can use
unu head zf1_tectum.nrrd
If not then cmtk’s describe gives you some of that info.
cmtk describe zf1_tectum.nrrd
Good luck!
Greg.