Hi Greg,
thanks for your quick reply!!!
The data is float greyscale. This is the shell:

C:\CMTK_Registration\CMTKreg>perl C:\CMTK_Registration\CMTK\bin\munger -b C:\CMTK_Registration\CMTK\bin -a -w -r 01 -T8 -X52 -C8 -G80 -R3 -A "--accuracy 0.4" -W "--accuracy 1.6" -s template/Ref20131120pt14pl2_Randlett_stackrev_01.nrrd images
hostname = Francesco-HP; short hostname = Francesco-HP
JOB ID =
Root directory is C:\CMTK_Registration\CMTKreg
Changing to root directory: C:\CMTK_Registration\CMTKreg
Setting image root to: images
MYEXEC: CMD = md Registration\affine\Ref20131120pt14pl2_MIP318zf01_9dof.list exited with value 0
Aff:MIP318zf01 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
MYEXEC: CMD = C:\CMTK_Registration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\Ref20131120pt14pl2_MIP318zf01_9dof.list template/Ref20131120pt14pl2_Randlett_stackrev_01.nrrd images/MIP318zf01.nrrd exited with value 255
Aff:MIP318zf01 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
MYEXEC: CMD = C:\CMTK_Registration\CMTK\bin\registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration\affine\Ref20131120pt14pl2_MIP318zf01_9dof.list template/Ref20131120pt14pl2_Randlett_stackrev_01.nrrd images/MIP318zf01.nrrd exited with value 255

Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images
Originally posted by Greg Jefferis: