I have had great success with Photoscan: I took a bunch of photos of a concretion containing a little bit of fossil bone, from all different angles, and uploaded them. The software aligned the photos based on common features, and created a 3D model!
At the end of it all, I hope to have all the concretions as 3D models, then I can fit them together to show how they form a large boulder. And inside hopefully lies a 90 million year old dinosaur fossil!