Dear Greg,

thanks for the quick reply. I used the most recent version of CMTK (3.2.3) and I tried it on a Mac and on a Windows machine using Cygwin.

Here is an example of my most recent command I used:

"/Applications/Fiji.app/bin/cmtk/munger" -b "/Applications/Fiji.app/bin/cmtk" -a -w -r 01 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 6 -s "template/template-1.nrrd" images

I'm pretty sure the error happens during the affine registration so I will try to play around with the parameters you suggested. Here is just an example of what I get:

1-12_12.33.42.command ; exit;
hostname = m-o0-033.neuro.mpg.de; short hostname = m-o0-033.neuro.mpg.de
JOB ID =
Root directory is /Users/mkunst/Documents/CMTK_Alignment
Changing to root directory: /Users/mkunst/Documents/CMTK_Alignment
Setting image root to: images
MYEXEC: CMD = mkdir -p Registration/affine/template-1_test_01_9dof.list exited with value 0
Aff:test_01 INFO: number of threads set to 6 according to environment variable CMTK_NUM_THREADS
Caught signal 11, faulty address is 0x190ec5000
[stack] Execution path:
[stack] 1 libsystem_platform.dylib 0x00007fff86a64eaa _sigtramp + 26
[stack] 2 ??? 0x00007fff5fbfda40 0x0 + 140734799796800
[stack] 3 registration 0x00000001000aaa9d _ZNK4cmtk13TemplateArrayIhE8GetRangeEv + 13
[stack] 4 registration 0x000000010005e222 _ZN4cmtk8VolumeIO4ReadERKSs + 2050
[stack] 5 registration 0x000000010005fd40 _ZN4cmtk8VolumeIO12ReadOrientedERKSsPKc + 32
[stack] 6 registration 0x000000010000512e _ZN4cmtk29AffineRegistrationCommandLineC2EiPPKc + 11294
[stack] 7 registration 0x0000000100002094 _Z6doMainiPPKc + 36
[stack] 8 registration 0x0000000100002210 main + 80
[stack] 9 registration 0x0000000100002064 start + 52
MYEXEC: CMD = /Applications/Fiji.app/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/template-1_test_01_9dof.list template/template-1.nrrd images/test_01.nrrd exited with value 1
Aff:test_01 INFO: number of threads set to 6 according to environment variable CMTK_NUM_THREADS
Caught signal 11, faulty address is 0x18fec5000
[stack] Execution path:
[stack] 1 libsystem_platform.dylib 0x00007fff86a64eaa _sigtramp + 26
[stack] 2 ??? 0x00007fff5fbfda40 0x0 + 140734799796800
[stack] 3 registration 0x00000001000aaa9d _ZNK4cmtk13TemplateArrayIhE8GetRangeEv + 13
[stack] 4 registration 0x000000010005e222 _ZN4cmtk8VolumeIO4ReadERKSs + 2050
[stack] 5 registration 0x000000010005fd40 _ZN4cmtk8VolumeIO12ReadOrientedERKSsPKc + 32
[stack] 6 registration 0x000000010000512e _ZN4cmtk29AffineRegistrationCommandLineC2EiPPKc + 11294
[stack] 7 registration 0x0000000100002094 _Z6doMainiPPKc + 36
[stack] 8 registration 0x0000000100002210 main + 80
[stack] 9 registration 0x0000000100002064 start + 52
MYEXEC: CMD = /Applications/Fiji.app/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/template-1_test_01_9dof.list template/template-1.nrrd images/test_01.nrrd exited with value 1

Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.
[Process completed]

Thanks,
Michael