DECA mean shape model: partly coarse surface

Community SlicerMorph
1

Hi,

I am using DECA for some shape analysis. I am wondering why the resulting reference / atlas shape model appears to have partly coarse surface.

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The workflow for comparing 2 groups looks like this:

  • first: using DeCAL to increase the number of points –> up to > 200 from initially manually 20 LM place of both groups
  • second: use the LM_aligned_200points and model_alignes_200points of one group to create an atlas using DECA
  • third: use this resulting atlas for comparing the shape variance between the atlas and the indiviual samples of group 2 using DECA

Maybe the initial number of manually placed LM is too less. Although I checked the initially aligned models based on the 20 LM –> they are well aligned with the resulting first base / reference.

Any idea how to improve the mesh of the reference model?

THANKS!

Best,
Markus

2

Do you have damage or missing parts in your input models?

3

Hi,

the models which are used are fine. No issues visible, size 40 MB after decimation, repair, normals recomputation and minor smoothing.

These data is used for generating the reference using DECA.

And the computed reference models are not similar affected showing more or less ripples.
Infact several reference models are derived from different starting data.

In short: the starting data seems to be fine.

Best,
Markus

4

Hi,

I repeated the compuation of the mean shape. This time I used the mouse data of the DECA tutorial. GitHub - SlicerMorph/Mouse_Models · GitHub

Again one can notice kind of rough surface. I am wondering where does this come from?
Mean shape of 60 skulls, I expect that there won´t be such edges / ripples generated.

Is this normal behaviour? I am wondering, such kind of “notch” is not visible in the skull data….

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Could you please comment on this mean shape outcome.

Thanks!

Best,
Markus

5

There shouldn’t be an artifact like that, unless one of the models have it. And I don’t think any of the models included in the sample data has a damage.

The other place it can possibly come is a mismatched landmarked that is warping the model incorrectly. Unfortunately as it is, DeCaL does not save the intermediate steps in the atlas creation. But DeCA does.

So use DeCa module to create the atlas from scratch one more time. Selections are very similar to DeCaL. Just make sure you enabled the “Create Output for Error checking” option. When you run DeCa this will create the folder errorChecking in the specified output folder where the warped models are saved. Load all of them into your scene, and see if there are any that appears warped incorrectly or have artifacts like that.

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