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Oct 26, 2019  03:10 PM | Nicholas Couturier - Case Western Reserve University
Converting to STL file

I am interested in 3D printing this model with the skull and cranial landmarks intact. Does anyone know how to convert this whole 3D model with the skull and brain into an STL file that I can use to 3D print?

Thank you
Oct 29, 2019  05:10 PM | Eszter Agnes Papp
RE: Converting to STL file
Hello Nicholas,

A few things to consider with regard to 3D printing of the Waxholm atlas:
  • You can generate STL files in ITK-SNAP by opening the atlas and the segmentation, and selecting which structures you want to save as STL (note: the resulting files can be pretty large).
  • We do not have a delineation of the skull, since it is hard to see its exact boundaries in MRI. One would typically use CT for such a task, which we don't have for this animal. If you need a skull model, you can either delineate it first and then print it (in this case, it would be awesome if you could share your skull delineation with the community), or choose another skull model, e.g. you can find a good one here:
  • As for the brain, if you want to 3D print the brain as a whole, you are best off using the binary brain mask here: WHS_SD_v2_brainmask_bin.nii.gz
  • Please note that STL models generated by ITK-SNAP are not optimized for 3D printing. You will likely need a few extra steps to correct the model before it can be printed. 3D printing is sensitive to e.g. holes and cracks between parts of the model. Also, if you choose to print multiple brain structures, there is a risk that they will not fit together as they should unless the models are optimized for this. Typically, printing bigger and bulkier structures (such as the whole brain) should work best. I suppose people at the 3D printing service you plan to use can help you with this (there is also a lot about it on the web, search for e.g. "optimize STL for 3D printing").
  • You can also try MeshGen for generating STL meshes that are optimized compared to "raw" meshes from ITK-SNAP: But be aware that we have had trouble printing some of these meshes too, so double check before you try to print.
Hope this helps!

Best regards,
Oct 29, 2019  06:10 PM | Nicholas Couturier - Case Western Reserve University
RE: Converting to STL file
Thank you for your response! I was wondering if it would be possible to 3D the whole brain enclosed in the skull from this dataset? I know the resolution of the skull isn't great however I only need the dimensions to be accurate (e.g. thickness). I am trying to print out a brain in a skull to implant electrodes into to determine stereotactic positioning prior to surgery. This would allow me to fabricate a custom electrode array with the electrodes already positioned where they need to be. Let me know if you have any ideas.
Oct 29, 2019  07:10 PM | Eszter Agnes Papp
RE: Converting to STL file