Hi Manuel -

This is just a wild guess, but it looks to me like there might be, in your original data, one slice that is a little brighter than the remaining slices.  When you reslice your data, say using a slight rotation, then the brighter slice appears to "travel" through the resulting stack as you scan through its slices.

You might be able to confirm this by scanning through your original data perpendicular to the brighter slice, but it might be too subtle to spot. If you have some way of doing a projection of your 3D stack onto a 2D plane (e.g., by maximum intensity project, or by averaging) then that might make the effect more obvious and help confirm this theory. I vaguely remembered that CMTK might have something to do that, but cannot find it right now, so it's possible that has been removed over the years.

Be that as it may, CMTK does have a "destripe" command line tool that might be able to correct this effect. Basically, its purpose is to identify slices in your data that deviate from the brightness of their neighbours, and adjust them accordingly. I haven't used this in well over a decade, obviously, so I don't have any specific suggestions for how to use the tool. But it might be fairly straightforward, so maybe give that a shot.

Best, Torsten