Hi Karel,
It looks like your mask file has a different image resolution than your brain images. That means there is no unique assignment possible between voxels in the mask and voxels in the brain images. You can solve this by resampling the mask to the brain size.
In case you don’t know how to change the voxel size, Kai wrote a script that does that for you, which you can find in the folder utils (tdtutil_change_voxelsize_or_bb.m)
Best,
Martin