Hey all,
I am struggling with the CMTK tool for a few days now. I finally got it running, however, the registration always fails to execute and it tells me "no such file or directory". I found a post from March 13, 2017, where exactly the same problem was described. However, no solution was suggested (or maybe I missed it).

The generated script is:

hostname = sarah-pc; short hostname = sarah-pc
JOB ID =
Root directory is /home/sarah/yourregistrationfolder
Changing to root directory: /home/sarah/yourregistrationfolder
Setting image root to: images
Aff:21OctSP8Fish1_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish1_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish1_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish3_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish3_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish3_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish4_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish4_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish4_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish2_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish2_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish2_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish1_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish1_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish1_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish3_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish3_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish3_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish4_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish4_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish4_01.nrrd failed to execute: No such file or directory
Aff:21OctSP8Fish2_01 MYEXEC: CMD = /home/sarah/Fiji.app/bin/cmtk/bin/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/Ref20131120pt14pl2_21OctSP8Fish2_01_9dof.list refbrain/Ref20131120pt14pl2.nrrd images/21OctSP8Fish2_01.nrrd failed to execute: No such file or directory

Ran 0 initial affine registrations of which 0 failed
Ran 8 affine registrations of which 8 failed
Ran 0 warp registrations
Reformatted 0 images

As suggested in the 2017 post, I have already checked with ls and all the nrrd files are where they are supposed to be...

I also have one additional question: I have 2 channels, one for tERK and one for pERK. Does it matter which one is 01 and which one is 02?

Best,
Sarah