If, on the other hand, I use a 16bit stack as floating image it works:

C:\CMTK_Registration\CMTKreg>C:\CMTK_Registration\CMTK\bin\reformatx -v --outputtype "ushort" --pv -o mylabels2.nrrd --floating C:\CMTK_Registration\CMTKreg\images\Stack_celllabels01.nrrd C:\CMTK_Registration\CMTKreg\template\Ref20131120pt14pl2_Randlett_stackrev_01.nrrd C:\CMTK_Registration\CMTKreg\results\Registration_318_vs_template\Registration\warp\Ref20131120pt14pl2_MIP318zf01_warp_m0g80c8e1e-1x52r3.list
Reading transformation from studylist C:\CMTK_Registration\CMTKreg\results\Registration_318_vs_template\Registration\warp\Ref20131120pt14pl2_MIP318zf01_warp_m0g80c8e1e-1x52r3.list
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: trying to change image coordinate space, but no current space is defined. Coordinate system of the resulting image is very likely incorrect.



If, on the other hand, I change to outputtype "uint" leaving everything else the same it does not work.