To check the file paths start the macro in Fiji, and take a look at the file paths under the "Input&Output options", if its empty choose the locations with the browse button first. For example for reference image it looks something like this , depending on where is yours   "C:\Users\admin\test_data\refbrain\JRC2018_UNISEX_20xHR.nrrd" , now check if there is any space character there, if yes change the folder or file name using your file explorer to do not contain spaces, then in the macro browse for the file or folder again before you run it. 

If further troubleshooting is needed use this test data

 https://www.dropbox.com/sh/54igm0xxmtlo4ei/AAA7EpGMZcoN_CMs8kG8zI26a?dl=0

-place test_data folder  on one of your internal hard drives directly like "C:\test_data" , use the images and the reference provided to run a registration.

-confirm that CMTK installed, open ubuntu terminal and type the command cmtk --help , after hitting enter you should see the cmtk help page.

- on windows 10 the macro has the limitation that it can just read files on the internal hard drives and not from network or external drive locations

Hope this will help.