Hi Thomas,

Your voxel sizes are not sensible and this is not going to help things.
In particular dx=dy ~= 0.013 cm while dz=1 cm ie ~ 77 deeper in Z than
wide in XY, the correct ratio is probably between 2 and 4. This means
that your brains are massively elongated in Z. You need to open the raw
confocal files (not exported tifs) in Fiji in order to get the correct
voxel sizes. If you cannot do this then use Fiji to set the Properties
for your tif files before saving to nrrd.

Regarding the lack of output file, I cannot really see what could be
wrong although I have no experience of CMTK on windows.

Best,

Greg.