Auto3dgm landmark placement on invisible parts of mesh

[raranda22]

Hello Slicer Community,

I’m using Auto3dgm on segmented upper beaks from MarkMyBird database, but it appears landmarks are being placed on seemingly invisible parts of the segmented meshes!

Here are the original unsegmented meshes:

Here’s how I segmented the meshes: I used Plane Cut tool in Dynamic Modeler, using a 2D plane placed vertically at approximately where the beak begins. I exported the desired segment as an .obj file. Interestingly, using either DeCAL or BUILDER module as part of ATLAS, they seem to respect the posterior boundary of the mesh (but they’re not without other issues with these meshes):

Any help would be greatly appreciated!

Best,

Ricardo Ely

[muratmaga]

I think that extension is abandoned, I don’t think anyone in the development team tracks this forum. You might try opening an issue on their github repo GitHub - ToothAndClaw/SlicerAuto3dgm: Repo for auto3dgm slicer extension but they don’t appear to be responsive.

I think if you use Dynamic modeler to cut a model, it removes the vertices but not the points. We encountered. that in other application. I opened an issue, Dynamic modeler ROI cut removes the polygons but not the vertices · Issue #8777 · Slicer/Slicer · GitHub

@lassoan maybe it is time to implement that clean option.

[lassoan (Andras Lasso)]

OK, I’ll add the clean option in the next few days.

[raranda22]

@lassoan That would be amazing, thank you!