Using ALPACA in 3DSilcer with data segmented in MeshLab

Hello Everyone,

I’m running into some trouble auto landmarking in 3DSilcer. I am trying to auto landmark the cleithrum of cichlids, and all the models that I am uploading into Slicer I have first segmented in Meshlab (I uploaded photos what what my specimen look like in MeshLab). I then set my source model, source landmark set, and my target model.
So where this get confusing is, I have loaded in only cleithrum files, but when I run ALPACA a point cloud of the whole fish skull renders (again I have photos below). Has anyone seen anything like this before? Could it be that I did not properly save my segmented files in Meshlab. My segmented cleithrum files are significantly smaller than the full skull files, could Meshlab be ‘hiding’ the rest of the fish skull instead of deleting unwanted elements.

Any help/ input would be very appreciated.


MeshLab probably removed cells (triangles), but did not actually remove the mesh points. You can use Surface Toolbox module’s Clean operation to remove unused points.