Mandible registration

Hi @erin_hong and @manjula

I agree with Manjula that the first step here is to see a bit more of what type of distances you have computed. Take into account that the color mapping in SPV by default will happen by setting your highest value in your distances to the color in your colorbar on the right and the lowest to the other end of the colorbar.

Could you please look at the attributes/ranges tab in SPV and see what is your min and max value in the distance map you have calculated, and let us know?


Please see two screenshots with values for attributes/ranges.



These are after I changed my range from -10 to 10.

Hi Erin,

You dont see much because you are visualizing the “normals” map. The magnitude of those maps goes from -1 to 1 (the magnitude of unit vectors pointing in or out)

In the attribute drop down menu, please change to “Signed”, there your values go from -8 to 8 mm (roughly). Play with changing the range to -5 to 5 and you should definitely see something.

Please let us know how it goes,

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In my screenshot above i have rounded in white where you need to change the attribute from normal to signed. Then changes the value range to -5 to 5 or far as it makes sense in the range section which i have pointed too.


Please see my screenshot below. The defect change especially #30 D is about 5mm so I should see more definite color(green or red) but I do not see it.

Please let me know!


Hi Lexus,

Can you please add a two points to the color map near the median with different color and move it around a bit.

If it does not work i guess there is some problem at Model to model distance measurement step or even at the registration step. If you could share some screenshots of the process or share your models some one might be able to help

Agreeing with Manjula here, continue saturating the color map (go down to -1,1, or lower) until you see something. It seems to be a difference in the crop between the two models, particularly in the mandibular area towards the chin and that is driving the most of the color interpolation.

Could you please take a snapshot of the two models overlayed with transparency and share that with us??

Thanks for the feedback!

May I have your email address? I will send you pre and post STL models via google drive. I can also share pre/post dicom files as well, if you want. Perhaps registration and hardening are issues as you both stated.

I will also send you screenshots of each step and send them. I would like to start from the dicom files.

Many thanks,


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Hi Erin,

I tried with your data. I think it works well. I did not do a good registration so the teeth are not well aligned. I think there is a error in your workflow. I will try to write the workflow in the afternoon.

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Looking forward to a more detailed workflow. Since I am working with CBCT scans not CT nor MRI, I was using Slicer CMF, FYI.



Hi all,

Manjula, thanks for that snapshot. The registration seems wrong, as illustrated for a pattern of positive distances parallel to the longest axis of the model. Erin, is it possible to see both of your models?

Also, have you tried to manually approximating your models to see if you can generate a better colormap?


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yes registration is wrong. i did not did the registration properly. it was just a quick test !

Hi @Lexus_H and @bpaniagua

Sorry i was bit busy.

I did use the models Erin send for registration with CMF Regis - surface registration

With max iterations and max landmarks.

Please see the video

The registration is not good. This is similar to problem i encountered with my previous work.

I solve my problem with cloud compare but i wanted to stick to one software for my work and i got good results with CMR- ROI registration.

In this case i did not do the ROI registration because i again encountered the bug that i reported on this some time back.

I use these models in cloud compare even with default setting i got good results.

please check the color maps with both registration methods

Erin i think you can try CMF ROI method. I think it should work pretty well.

Also since you have DICOM data why don’t you do the Image registration (General Registration -BRAINS) and then do the segmentation. Then your segments will be created properly registered. It would be great if @bpaniagua or Prof @lassoan can tell further about this.

Is registration on DICOM will be more accurate than registering the Surface models/Segments ?

Despite the answer to me previously by Prof Lasso on registration i am still baffled by the accuracy of cloud compare registration over CMF Surface registration. :star_struck:

In any case the problem that we set out to see seems like you are not measuring the model to model distance properly. Please see the video.

Image registration would try to align soft tissues as well, so you would need to apply masking, but that would be essentially the same kind of thresholding that you do to extract the surface. Image-based registration would be also more vulnerable to image artifacts (due to presence of metals). So, unless you register a small region, such as a single tooth, surface registration is probably more appropriate. It also allows you to use the same method to register CBCT/CBCT and CBCT/intra-oral surface scan.

Rigid surface registration of low-noise surfaces with good initialization is trivial, using ICP. Maybe the problem is that the cut surface is included in the registration, which of course must be excluded because they are not exactly the same on the two models. If you cut those off (leaving the cut-off ends open) then registration must be accurate.

It would be nice to add a surface selection tool to SlicerCMF that would allow to select a part of a surface for registration.

Thank you for the explanations. First questions is answered understood.

With regard to second question i am not sure what you meant by the cut surface ?

In any case the way i understood was the anterior and posterior ends of the mandible.

So i just clipped around the teeth and did the CMF surface registration with 4000 iterations and the results were much better. Then i applied the transform to the whole model and got a much better color map. I dont know is that what you meant.

And ofcourse if we can select the surface then it will absolutely solve this problem i guess… :grinning:

This is surface registration which I could not get it to register well. Please notice the transparent model that did not superimpose well.

This is a registered post defect model with CMF fiducial registration which I believe, works better than ROI. Do I have to see transparent gray for pre defect model?

Dr. P, yes I manually approximated before I segmented both images then created STL for surface registration, in this case, I used fiducial registration.

Even Prof. Lassoan stated that I should use surface registration but somehow surface registration is not giving me a good result. Also, I even clipped to make the two models more even at the borders(distal to molars and mesial to anteriors)

Hi Manjula, I will try general registration using DICOM files. your recommended video clip does not have voice recorded so it is kind of hard for me to follow. Also, should I use slicer CMF for general registration or just slicer?

Can you also explain to me what cloud compare is?

Many thanks,

If anyone is willing to try with dicom files to evaluate whether my work step was OK or not, please let me know, I can transfer them via google drive link. Since I sent my stls and my registered and clipped model and model to model is simply plugging your models in order to generate vtk file for SPV, I do not know what I’m doing wrong. Only the periodontal defect is the change and that should be colored based on the depth and allocated color in the color bar not the rest of the mandible (teeth can move bc it is dry mandible but not as much as defect sizes up to 9mm).

Hi Manjula,

Are you able to send me the surface registered model to me so I can play around with it to see if the periodontal bone defect matches my gold standard?

Since I just realized that your maximum was -4 to 4, it colored the same as red.

I believe you have my email address from the google drive link.



Hi Manjula,

This is a color map page using slicer CMF 5.0 that i generated using Manjula’s registered models using cloud compare. Not much better as you can see.

Well i think you are not doing it properly somewhere because this is what you should see if done correctly

Also you need to change the attribute to signed and also the figure you see is just a scale not in millimeters or anything.
x 0.5 is the center (Superimposed) and to either side you get the deviation by the percentage.

if the range is for e.g -5 to 5 in mm then at ever 0.1 position you will move 1 mm + or -