After a couple of recent enquiries, I thought I would post a link here to the user documentation and examples of CMTK usage that my lab maintains:

http://jefferislab.org/warping

In addition to using CMTK directly, we have written a number of tools to wrap CMTK, including a script called "munger" that is now distributed directly with CMTK and coordinates large numbers of registrations. We have also provided a simple GUI for mac and more recently a cross-platform GUI based on Fiji/ImageJ. Finally we have written code for R which we use for image analysis and e.g. transforming neurons from one brain to another or from left to right. This is available here:

http://github.com/jefferis/AnalysisSuite

Obviously all of this is completely unofficial, not supported by the CMTK team etc, but is of use to at least some CMTK users. Feel free to contact me for further details. 

Best wishes,

Greg.

--
Gregory Jefferis, PhD
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-lead...
http://jefferislab.org

Thanks Greg - this is awesome :)

TR

Thank you for these nice additions, they're really useful. I tried munger in Linux and it worked just fine. However I wasn't able to make it work on Windows (even tweaking the script). Does it work on Windows? I can perfectly live with it, but I just want to make sure I'm not missing anything.

Thanks for the help.

All the best,

Jose

Jose:

From the top of my head, I can think of two ways to get munger to run on Windows:

a) you can install Cygwin and build and run CMTK under that environment. This should essentially behave like a lightweight "Linux inside Windows"

b) if you want to run CMTK and munger natively on Windows, you need to install Perl for Windows. Did you do that? If that doesn't work for you, I'd suggest falling back to option a).

Best,
Torsten

Thank you very much for your answer.

a) This option should work. I'll give it a try.

b) Indeed I installed Perl. The problem, as far as I understood, has to do with native unix commands called from inside the script (which should be solved by a).

Thanks again and all the best,

Jose

Originally posted by Jose Cruz: Indeed - I am afraid there are a number of commands used in the script which are more or less unix/linux specific

e.g.

which
mkdir
find
gzip

At some point these should be converted to generic perl, but I am sorting of waiting for a keen windows user to make the running!

Best,

Greg.

Just to add that courtesy of Martin Trapp at VRVis, munger has now been patched (svn r5055) to run on Windows. I have not been able to test myself, so user testing would be appreciated. Best,

Greg.