Hi Thomas:

You know of course there are no stupid question - just stupid answers ;)

Since you're asking about tiff and multiple color channels, let me start by pointing out that CMTK cannot handle 2D data, only 3D, and it cannot handle vector-valued data, such as RGB. Just to get these two out of the way.

I usually use the ConvertBetweenImageFormats tool from ITK's companion "InsightApplications" to convert file formats, but ImageJ should work at least as well.

Now for your specific problems:

a) unfortunately you found a typo in the CMTK User Guide - the registration tool has an option "--auto-multi-levels", not "--auto-multi-level" as it says in the guide. I will fix that in the next revision. Simply change your command line by adding the missing "s" and things should work.

As a general suggestion - all tools in CMTK support the "--help" option, which will print a list of all supported command line options for that particular tool.

b) the problem you have with "warp" is probably related to the fact that the preceding "registration" command failed and did not actually generate any output file at all. What's a bit curious, though is that the error message for a non-existing input transformation should say that it doesn't exist, not that it is in an unsupported format. If the problem persists after fixing the "registration" command, feel free to send me the "affine.xform" contents (this is most likely a directory) and I'll take a closer look.

Best,
 Torsten
Originally posted by Thomas Templier: