I use Meshlab to make final meshes from my surface scans–deleting unwanted parts via surface painting or drawing boxes, aligning scans or parts, flip normals, Poisson surface reconstruction for a watertight mesh, decimation, smoothing, adding color/shading. I can quickly toggle vertex colors or textures on/off and transfer them between meshes. I also apply Ambient Occlusion shading for pathological CT/microCT specimens to highlight the surface details and use the same function to remove internal surfaces if needed.
Even compared to Meshmixer, the manual alignment in Meshlab is easier for me–I can select a single axis to translate/rotate or just click on the model and move it (I usually need this to align separate pieces or 2 surfaces of a flat object). The ICP alignment using 4 or more points is quick and sometimes works for articulating matching edges on fragments or sutures.
I have my workflows down for Meshlab, so it’s just a matter of sitting down with Slicer to see if I can do the same things. For the microCT models, I have started using the Surface Toolbox more than Meshlab to decimate. And I really use a combination of Slicer, Meshlab, and Meshmixer for surface scans and CT/microCT models, depending on what I need!
I have recently started working with post-autopsy CT scans so the areas of interest are not in the correct places. I know I can use Split Volumes in the Segment Editor to create separate volumes for each segment but can I then move these to the correct anatomical positions and then create a new CT volume? I can move the exported models in Meshlab, but then the CT volume doesn’t match. I don’t know at this point if I need the CT volume to match the 3D models, but for these cases it would be nice to have the full workflow in Slicer.