I am wondering if you have any suggestions for me on how to tackle this task in 3D Slicer. I have four genotypes of mice for a rather complex phenotype, and want to visualize the differences in BMD across all the bones of the skull. Specimens were scanned alongside a hydroxy apatite phantom. I would also like to show differences in bone thickness in a separate figure - as this may or may not correspond with the BMD of a bone but may instead reflect disorganization of bone growth. Thank you!
Visualization is the easy part; i.e., as long as you can convert the intensities in voxels to BMD using your phantom. Once you get that, you can make a 3D segmentation of your skull, and use the “Probe Volume with a Model” that’s one option (volume in this case being the BMD values for that skull).