Hello! I am seeking advice on how to practically reconstruct a skull in order to calculate cranial capacity. The skull is a fragment (missing skull base and some parietal), estimated to be a 4 year old indiviual. I have segmented complete skulls of 4 year olds from NMDID CT scans and aligned them…

If anyone has further advice on this regarding a workflow I would be very grateful! @muratmaga @lassoan @pieper

Quick or Affine are not deformable registrations. Quick simply rotates and translates the object, affine does the same with scaling and shearing allowed. You need deformable registration to warp one object to the other, and that’s computationally expensive and long. So, if you want to run things fa…

Thank you. This has been my procedure and parameters so far: (1) Group-Wise Tab: Template: case-109181_skull.nrrd. Output: Transformed Volume. transform Type: antsRegistrationSyNQuick[s] (~30 mins / volume). (2) Then in the Template tab: Initital Template: case-109181_skull.nrrd Transform Ty…

I recently created a module for reconstructing fractured orbit using the mirrored contralateral side built on functions from SlicerMorph. I wonder if the two sides are similar enough to warrant a good registration, but it might not hurt to give it a quick try. You can one-click install SlicerOrbit…

I don [image] ThomasVanParys: (2) Then in the Template tab: If you are going to use my suggested approach, which is find 3-4 age/sex matched normal skulls, and segment the endocranial space from them, and then deformably register them to your fractured one, then you don’t need to use the tem…

Great, I will try this. A potential issue, however, is that the fragmented skull is just an .obj surface mesh. Converting this to a segmentation → Export models and labelmaps → Export to new labelmap, creates anomalies and artefacts in the volume (bottom: surface mesh, top: labelmap volume in 3D re…

Would you be able to fill it using something like SurfaceWrapSolidify? [image] Fill or extract cavities in segmentations using the new "Wrap Solidify" effect Support Making a segment that has fractured, discontinuous boundary and holes inside to be a simple so…

How did you generate the obj? You don’t have the original scan? That’s what you will need for this to work. Even if you were to able to generate a decent labelmap by cleaning up, registration will not work, as it expects and intensity image.

That’s a huge shame! I believe it was made via photogrammetry/Artec Spider work…

We will have to CT scan the Crania when we are next in the field - but is there any possible method to use the .obj alone?

Reconstructing a skull fragment with SSM/PDM

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chz31 (Chi Zhang) December 5, 2025, 6:34pm 16

Would you be able to fill it using something like SurfaceWrapSolidify?

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Reconstructing a skull fragment with SSM/PDM

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