Hello, I am a new user to CMTK. I tried to install FIJI plugin of CMTK following the instructions on the github page of fiji-cmtk-gui, however, the folder Fiji.app/bin/cmtk is always empty no matter which version of CMTK I try and how many times I update/restart my FIJI. I also tried the developer install, but the problem persists. Has anybody encountered the same issue before? Thanks!

--Dan

Hi Dan,

I�m afraid that the jython version bundled with Fiji changes periodically and each new version seems to have bugs that cause problems for fiji-cmtk-gui. I have not tried to fix these for the latest version of Fiji but I will try to look sometime after Wed. It would be helpful to know which operating system you are running on.

Best wishes,

Greg.

Thanks Greg! I am currently running on Ubuntu 16.04. Is there any chance that I can use CMTK while bypassing FIJI?

Absolutlely. The Fiji cmtk gui is just designed to help make scripts to run CMTK jobs using the munger script which coordinates registration and reformatting for large sets of input images. But you do not need to use cmtk gui or the munger script with CMTK.

Best,

Greg.

Just to add to what Greg is saying - if you do decide to try and run CMTK directly, there are several pieces of documentation that might help you:

https://www.nitrc.org/docman/index.php?g...

One of these is a general user guide covering mostly registration and reslicing. The other two deal with two very specific applications, unwarping of structural and echo-planar MRI.

Also, all CMTK tools will give you a summary of their available command line options when you call them with "--help"; in some cases, advanced options will only be shown with "--help-all", to keep the initial help output a little less cluttered.

Hope this helps.

Best,
  Torsten

Thanks Torsten! I installed cmtk with sudo apt-get and find all the tools under /usr/lib/cmtk/bin, tried a few commands and it seems functioning. However, I cannot launch cmtk directly from terminal. Typing "cmtk" in bash pops a message "/usr/bin/cmtk: line 49: /usr/lib/cmtk/bin/: Is a directory". I have to enter the folder /usr/lib/cmtk/bin to access any function there. This may sound silly, but Is it possible to launch cmtk directly from terminal?

Best,
Dan

Hi Dan -

I think that's a misunderstanding ;)

"cmtk" isn't actually a tool in and of itself, but simply a convenience wrapper to call specific tools without having to use their path.

So instead of "/usr/local/lib/cmtk-3.x.x/bin/registration" (or wherever the tools actually get installed these days), you can just use "cmtk registration ..."

But by itself, "cmtk" doesn't do anything (except give a cryptic error message, apparently).

Torsten

I had a patch that would at least give a list of all the possible commands. We should apply sometime for this reason.

Greg.

https://github.com/jefferis/cmtk/pull/1

Sounds good.

Thanks Torsten!  "cmtk " works. :)

Best,
Dan