NITRC Computational Morphometry Toolkit (CMTK) Forum: users

RE: CMTK Registration Warp Failure

Sandor Kovacs — Fri, 30 Oct 2026 9:13:52 GMT

Hey, Sorry the forum wasn't working for a while, propably I can only help you if i can see the data, just the anatomy channel is enough. Share a Dropbox link or send an email to the madi3d contact address.

RE: CMTK Registration Warp Failure

keanumchandra — Wed, 21 Oct 2026 20:00:57 GMT

Thank you for the suggestions.

I have followed your pipeline of pre-alignment and used the Wiki parameters to try and adjust my output to no avail. Here is a list of the parameters I have already tried changing.

Initial Alignment changed from Current Pose to Volume Center
Tried both Anisotropic Scale and Affine Transform

Changed Grid Spacing from 80 to 120

Decreased and increased energy weight
Set Jacobian Weight to 0.1

Set Inverse Consistency Weight to 0.1

Turned on final full-resolution warp optimization.

Are there any other parameters or pipeline changes I can make to achieve alignment that actual expands the top and bottom of my sample brains to fit the reference one?

Thank You

RE: CMTK Registration Warp Failure

Sandor Kovacs — Mon, 19 Oct 2026 9:55:19 GMT

It looks like your samples are suffering from severe local distortion or folding. If you run an affine only registration and reformat, you should already see reasonably good alignment. Otherwise, the subsequent nonlinear warp may produce distorted results.

Greg's wiki provides a good assessment of registration parameters and their outcomes:

https://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:start

Registration also has its limits when dealing with distorted samples. MADI3D can help push these limits a bit through interactive manual prealignment, allowing you to translate, rotate, and independently scale your sample along the X, Y, and Z axes before running registration.

Here's the workflow in a nutshell:

First, make sure your sample is loaded into the scene either as a multichannel volume or as individual channels organized into their own group.

Make sure both the template and the sample are visible in the 3D view. Select the group containing your sample channels, or the multichannel volume itself. This ensures that the same transformation is applied consistently.

Open the Transform panel and manually align your sample while inspecting the scene. You can also enable the interactive transform widget. Try to achieve reasonable overall alignment.
Once you're satisfied with the pre-alignment, open the Registration panel. The easiest way to set up the reference is to right-click the template in the scene tree and select"Add as Template to Registration". Then add your sample as well.

Check that the channel roles (especially the Moving registration channel role for the channel you use for registration with the template), registration inputs, and reformat settings are correctly assigned. You can also specify a custom registration output location if desired.

Finally, run the registration.

RE: CMTK Registration Warp Failure

keanumchandra — Mon, 19 Oct 2026 0:59:20 GMT

Thank you for introducing me to this amazing tool! I do have a few issues I am experiencing with registration in MADI3D that I was hoping you could identify. 1. When the brain I want to align needs to be Z-flipped to match the reference brain, I will Z-flip in Fiji and run CMTK registration that way. However the output is always heavily skewed when I do this, is there a reason why? 2. When alignment is successful I do get large voids in the earlier and later stack layers. Is there any way to remedy this issue. I have attached an example of what I am talking about below. 3. Finally I would like to mention that after running alignment to the reference brain the top part of the brain is not being pulled out to match the reference brain. Our brains have been slightly squised because of the slides so I was wondering if this is an issue that CMTK registration can fix or not. Thank you once again!

RE: CMTK Registration Warp Failure

keanumchandra — Mon, 12 Oct 2026 8:10:11 GMT

Thank you for the response Sandor Kovacs. It actually turns out the issue was not my naming conventions but actually my brain orientations. The brain was not rotated to match the reference brain which ended up causing a warp failure. Unfortunately the aligment was not perfect and my aligned brains have several dark gaps in them especially on the early and later layers. I am not sure if you know why that may be but I will try it with the new CMTK GUI integration which might fix the issues I currently have.

RE: CMTK Registration Warp Failure

Sandor Kovacs — Sat, 10 Oct 2026 9:03:10 GMT

Also I have a new CMTK GUI integration which may be more helpful to you. The idea was to integrate CMTK into a 3d rendering and editing environment while keep it native. Geometry, grid and transforms are directly tranlated into CMTK conventions, also data is processed as raw arrays into CMTK input so no compatibility and naming concerns. The main idea is that you can see the same physical pose and intensities as CMTK would receive so you can make better judgment on your data and the parameters, also you can easily and interactively pre align your data with the manual transform tool.

get it from here, windows store version is the most convinient option at the moment, but mac and ubuntu is also supported:

https://madi3d.org

It is still beta but it should be stable enough for your purposes, also the registration modul is open sourced on github so you can validate the math.

RE: CMTK Registration Warp Failure

Sandor Kovacs — Thu, 08 Oct 2026 18:55:36 GMT

Hi, 
By the first look of it, you have to make sure to follow the naming convention specified in the user guide (see the github page readme)
So reference channel should have the _01 suffix and so on up to channel _04. Tell us if that helped.

CMTK Registration Warp Failure

keanumchandra — Wed, 07 Oct 2026 15:46:42 GMT

Hello, I am currently experience a "Registration warp failed" message when attempting CMTK registration. I am currently using the Parallel-Fiji-CMTK registration script provided here https://github.com/sandorbx/Parallel-Fiji-CMTK-Registration. I have successfully used some of the test fly brain files provided so I presume this is an issue specific to the fly braint nrrd files I am currently using. Here are the log results and dimensions of the file I am currently using. If anybody can provide advice on how to remedy this issue that would be greatly appreciated. File dimensions: Width:  748.8000 microns (2304) Height:  748.8000 microns (2304) Depth:  126 microns (210)
Reference File dimensions: Width:  627.76 microns (1652) Height:  291.8400 microns (768) Depth:  182.02 microns (479) LOGS:______________________________
Detected operating system: Windows 11 (windows) WSL/CMTK validated Started Affine and Warp Registration on 1 samples Preset: Full Flybrain(Cachero-Ostrovksy_2010)   Affine parameters: Initial affine method: --centers-of-mass Affine registration metric: Normalized Mutual Information Exploration [Initial optimizer step size]: 16 Accuracy [Final optimizer step size]: 0.8 Degrees of freedom first pass: 6 Degrees of freedom second pass: 9
Warp parameters: Warp registration metric: Normalized Mutual Information initial exploration step size: 26 Accuracy [Final exploration step size]: 0.4 coarsest resampling: 8 Refine grid: 4 grid size: 80 Please wait WARNING: image does not have valid orientation meta information; cannot reorient. WARNING: image does not have valid orientation meta information; cannot reorient. WARNING: image does not have valid orientation meta information; cannot reorient. WARNING: image does not have valid orientation meta information; cannot reorient. WARNING: image does not have valid orientation meta information; cannot reorient. WARNING: image does not have valid orientation meta information; cannot reorient.   37F06-49F04_ALdown_B007 Registration warp failed

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