Creating a 3d model from MRI files

Hi all, a friend of mine was in an accident that caused her height loss in one of her vertebrae. Her birthday is coming up so I thought it’d be fun to giver her a 3D print of her broken spine. I have her MRIs and watched a few 3D Slicer tutorials but my files dont seem to be working right.

It looks like it imported everything to the DB correctly but the views look weird. Theres 1 view that looks fine and then the top and right side view are only thin blurry strips. (It said there were errors to see in advanced view?) Also most tutorials seem to be using CT files that have an obvious contrast for the bones but the MRI files I have dont seem to have the same thing. Is there anything I can do with this?

Thanks for any help!

When MRs are acquired they often save time by acquiring anisotropic data. There’s some more description and some suggestions here:

Hey Sythic, what you have there looks like a 2mm slice CT scan. I’ve created spinal models from what you have before. Using mainly the sagittal view (yellow) that you have and the FastGrowCutEffect add-on. the DICOM has been generated from the sagittal view, so it has a high resolution, but every 2mm. This means you have voxels that are rectangular. Take you time with FastGrowCutEffect to teach it the anatomy you want. You could try just thresholding but I’ve found those models take longer to clean up. Once you have exposed your stl model, import to MeshMixer and remove all the geometry that looks undesirable, spikes and voids. Remove any internal geometry of the model that you don’t need, then smooth the entire model to remove the CT slice lines. For your gift purpose this will look great.

Regards, Matt

Note that since Slicer-4.8, Segment editor module should be used for segmentation instead of the old Editor module. Segment editor module has fundamental changes, many improvements and fixes. It has a completely reworked, much faster and easier-to-use grow-cut effect: Grow from seeds effect. It also has Smoothing effect with several options to make surfaces smoother; and Scissors and Islands effect to remove irrelevant parts of the segmentation.

Hey guys, thanks for the great tips. I actually got another disc of a much higher res MRI/CT she did which had like 500 layers and the bones were properly contrasted. It’s not perfect but pretty happy with how it came out without any tedious rotoscoping each layer.