NITRC Computational Morphometry Toolkit (CMTK) Forum: users

RE: Original CMTK GUI and Parallel CMTK GUI not working on Mac 13.7.8

Tristan Stoyanof — Sun, 16 Aug 2026 17:28:24 GMT

Thank you so much! I'll give it a try this week and report back. We ended up dedicating a Windows PC to CMTK in the meantime, and it was much easier to set up (once I figured out I needed WSL 2 installed).
I'll see if I can get it working on the Mac, and at the very least be the guinea pig for this new set of instructions. I'm moving to a new lab soon, but I'll make sure the next user gets all this too!

RE: Current CMTK instructions for non-coders?

Sandor Kovacs — Sun, 16 Aug 2026 14:26:29 GMT

Hey, I found some time to look into this. Hopeully this will fix the mac issues: https://github.com/sandorbx/Parallel-Fiji-CMTK-Registration/tree/fix/mac-cmtk-discovery

RE: Original CMTK GUI and Parallel CMTK GUI not working on Mac 13.7.8

Sandor Kovacs — Sun, 16 Aug 2026 14:24:03 GMT

Hi,  I added some changes, there are now automatic and manual tools to help the user discover the right cmtk binaries. It may not be the solution but worth testing: https://github.com/sandorbx/Parallel-Fiji-CMTK-Registration/tree/fix/mac-cmtk-discovery Please report back either way, Thank you!

RE: Original CMTK GUI and Parallel CMTK GUI not working on Mac 13.7.8

Tristan Stoyanof — Fri, 07 Aug 2026 16:48:37 GMT

Originally posted by Sandor Kovacs:
<blockquote>
Hi, 
The Mac Version is a bit neglected at this point, I dont have the hardware currently, you can help with a bit of troubleshooting though. Can you try to run a simple cmtk command like cmtk - - help, or something from the CMTK user guide by Torsten and tell us the result? Also can you tell me the path of the CMTK/bin folder? Thanks! 
</blockquote>
I apologize because I'm very non-tech savvy. I downloaded the newer CMTK that Greg pointed to, when unzipped it becomes a .dmg file. Within, there's a CMTK folder and instructions to move it to the Applications folder, which I've done. I've also moved a copy of that new CMTK folder to Desktop/Fiji/bin/CMTK, but I'm not tech literate enough to know how to use this updated CMTK donwload correctly. Additionally, I was struggling to get the cmtk --help command to work, even after changing the directory to those two I just described.
Thanks again for the help and patience!

RE: Original CMTK GUI and Parallel CMTK GUI not working on Mac 13.7.8

Greg Jefferis — Fri, 07 Aug 2026 8:44:54 GMT

The unofficial GitHub repo now includes regular builds for Mac and Linux. If you have trouble with the Mac build from nitrc this could be helpful 
https://github.com/jefferis/cmtk/tree/natdev best,
greg.

RE: Original CMTK GUI and Parallel CMTK GUI not working on Mac 13.7.8

Sandor Kovacs — Fri, 07 Aug 2026 8:35:28 GMT

Hi, 
The Mac Version is a bit neglected at this point, I dont have the hardware currently, you can help with a bit of troubleshooting though. Can you try to run a simple cmtk command like cmtk - - help, or something from the CMTK user guide by Torsten and tell us the result? Also can you tell me the path of the CMTK/bin folder? Thanks!

Original CMTK GUI and Parallel CMTK GUI not working on Mac 13.7.8

Tristan Stoyanof — Thu, 06 Aug 2026 18:37:00 GMT

Hi All,
We had historically used the Jeffries CMTK GUI on our Mac, but a recent forced IT update has thrown it all out of whack. When using it, it generates a "commands" folder as normal, but won't populate it with a written script.
I then tried the newer parallel GUI, using the "Full Flybrain" + "Affine and Warp Registration" options and settings similar to what we've run in the past, even though most of the settings won't change when using the preset (we've used the OG GUI to register zebrafish brains numerous times). Whenever I run that, both the warp and affine steps immediately fail, and so zero images are reformatted.
I've checked the folder/file naming conventions. There are no spaces, no underscores except for just before the channel names, and no special characters. Any clue as to what could be driving the issues?
The OS is Ventura 13.7.8, and all of the CMTK files seem to be the most updated versions possible. I appreciate any help possible!

RE: Current CMTK instructions for non-coders?

mwu — Mon, 27 Apr 2026 20:49:04 GMT

Thank you very much.  I will try these and let you know how that works out for us.

RE: Current CMTK instructions for non-coders?

mwu — Mon, 27 Apr 2026 20:48:20 GMT

Thank you for taking the time to try to figure this out for me.  I appreicate it!  I will try installing on a PC and see if that works for me.

RE: Current CMTK instructions for non-coders?

Greg Jefferis — Wed, 22 Apr 2026 23:30:19 GMT

There are now automated binary builds on my unofficial github repo for CMTK. Next time you need to install maybe you could try them out and feed back if they work for you. Best, Greg.
https://github.com/jefferis/cmtk/tree/natdev https://github.com/jefferis/cmtk/releases/tag/natdev-latest