Hi all,
I am new to CMTK. I ran a trial registration with test data from the jeffris lab wiki.  
The script is still running but I am worried about an error it shows:
WARNING: trying to change image coordinate space, but no current space is defined. Coordinate system of the resulting image is very likely incorrect.
Would this affect the quality of registration? If so, how do I fix it?
Ideally, I want to avoid using the command line version.
Thank you!

Don't worry - this warning is harmless. The test image data does not have an anatomically defined image space like the RAS or LPS typically used in human imaging studies.

Best,

Greg.

Hi Greg,
Thanks for your prompt reply. I have another question:
The test data on your lab wiki has only ch_01 images. I assume that means that they are all the nc82 channel. 
When I ran the registration script and looked at the merged reformatted image for JFRC2_TNB9R-GH14601_warp_m0g80c8e1e-1x26r4.nrrd and the JFRC2.nrrd reference brain, the two colors don't overlap. I've attached the composite file in .nrrd format. 
I am completely new to brain registration so please pardon the naive questions. 
Thanks! 
Sneha