Hi Torsten,

Thank you so much for spending time to rebuild the package! I appreciate your help. Now the incompatibility disappears, but the package cannot find my data files. 

My working folder is: D:\Data\cmtkRegistration
which originally contains three folders: 
D:\Data\cmtkRegistration\commands (generated by CMTK GUI)
D:\Data\cmtkRegistration\images (created by me, contains two image stacks FBZD01.nrrd, FBZD02.nrrd)
D:\Data\cmtkRegistration\refbrain (created by me, contains one reference image Nov012016B3ZDref.nrrd)

Since my FIJI cmtk plugin fails, I manually changed the paths of munger and cmtk in a previous munger script, so the script becomes:

#!/bin/sh
# 2017-03-14_10.13.30
cd "D:\Data\cmtkRegistration"
"C:\cygwin64\usr\local\bin\munger" -b "C:\cygwin64\usr\local\bin\cmtk" -a -w -r 010203 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 1 -s "refbrain\Nov012016B3ZDref.nrrd" images

Running the munger script yields the error message: 

$ sh munger_2017-03-14_10.13.30.sh
hostname = Admin-PC; short hostname = Admin-PC
JOB ID =
Root directory is /d/Data/cmtkRegistration
Changing to root directory: /d/Data/cmtkRegistration
Setting image root to: images
Aff:FBZD01 MYEXEC: CMD = C:/cygwin64/usr/local/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/refbrain/Nov012016B3ZDref_FBZD01_9dof.list refbrain\Nov012016B3ZDref.nrrd images/FBZD01.nrrd failed to execute: No such file or directory
Aff:FBZD01 MYEXEC: CMD = C:/cygwin64/usr/local/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/refbrain/Nov012016B3ZDref_FBZD01_9dof.list refbrain\Nov012016B3ZDref.nrrd images/FBZD01.nrrd failed to execute: No such file or directory

Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images

The "Registration" folder is created upon the execution, which means it can recognize my working folder. However, the program insists that my image files don't exist. Do you have any idea what went wrong? 

Best,
Dan