Hi Sandor,

I re-installed ubuntu (I think it wasn't installed correctly) and ran CMTK registration on the test data again. It returned reformatted images for channels 1 and 3. Here is what I found after pasting the log onto the ubuntu terminal - 

WARNING: image does not have valid orientation meta information; cannot reorient.
/usr/bin/cmtk: line 50: 1632 Killed ${CMDPATH} "$@"
WARNING: trying to change image coordinate space, but no current space is defined. Coordinate system of the resulting image is very likely incorrect.
WARNING: trying to change image coordinate space, but no current space is defined. Coordinate system of the resulting image is very likely incorrect.
[1]- Exit 137 cmtk reformatx --pad-out 0 -o /mnt/c/Users/sheet/Documents/test_data/gehirn_Registration_2022-9-11-15-47/Reformatted/warp_gehirn_01.nrrd --floating /mnt/c/Users/sheet/Documents/test_data/images/gehirn_01.PIC /mnt/c/Users/sheet/Documents/test_data/refbrain/JRC2018_UNISEX_20xHR.nrrd /mnt/c/Users/sheet/Documents/test_data/gehirn_Registration_2022-9-11-15-47/gehirn_warp.list

I performed the registration with my images, but I could neither register not reformat, but essentially got the same error.

WARNING: image does not have valid orientation meta information; cannot reorient.
/usr/bin/cmtk: line 50: 1845 Killed ${CMDPATH} "$@"
/usr/bin/cmtk: line 50: 1844 Killed ${CMDPATH} "$@"
[2]+ Exit 137 cmtk reformatx --pad-out 0 -o /mnt/c/Users/sheet/Documents/registration/file_Registration_2022-9-11-16-22/Reformatted/warp_file_02.nrrd --floating /mnt/c/Users/sheet/Documents/registration/images/file_02.nrrd /mnt/c/Users/sheet/Documents/registration/refbrain/refbrain.nrrd /mnt/c/Users/sheet/Documents/registration/file_Registration_2022-9-11-16-22/file_warp.list
spotdar@SheeDell:~$ WARNING: trying to change image coordinate space, but no current space is defined. Coordinate system of the resulting image is very likely incorrect.


[1]+ Done cmtk reformatx --pad-out 0 -o /mnt/c/Users/sheet/Documents/registration/file_Registration_2022-9-11-16-22/Reformatted/warp_file_01.nrrd --floating /mnt/c/Users/sheet/Documents/registration/images/file_01.nrrd /mnt/c/Users/sheet/Documents/registration/refbrain/refbrain.nrrd /mnt/c/Users/sheet/Documents/registration/file_Registration_2022-9-11-16-22/file_warp.list

Thoughts?