Hi @lydian,
Thank you very much for your help.
I was opening the annotation atlas NRRD file with ImageJ and saving it as a TIFF file (don’t do that!).
Accessing the annotation atlas NRRD file directly with SimpleITK, as you suggested, did the trick and solved my annotation problem.
As mentioned in CCFv3 annotation: wrong IDs - #4 by NicoKiaru, ImageJ fails to handle biggest integers properly because uint32 (which range from 0 to 4 294 967 295 = 2^32 -1) are converted into float32 (not precise enough for integers above 16 777 215 = 2^24 - 1).