Tuesday, October 16, 2018

3D Model Extracted From CT Scan

More stuff moved over from my old web site.... Just in time for Halloween!

In 2007, when I was in dental school, I had a cone beam CT scan done.  I was going to have braces put on my teeth and I had a dental implant at #3 and I think they wanted to check the implant status before attaching brackets to my teeth.

After the scan was done, the radiology tech showed me the visualization capabilities of the software.  It was very impressive.  I had been reading about 3D printers for years and decided that I wanted a copy of the CT scan data because I planned to be able to print it some day, so the tech burned the data to a CD (remember those?) for me.

Six years later, and I had built MegaMax, my first 3D printer.  I located the CD with the CT scan data and went to work on finding free software that would allow me to extract data and produce a printable model.  It was a real project at the time- there were only a few free packages that could do the job.  I think I spent a total of about 40 hours hunting for software, then learning how to use it, and finally extracting the model and cleaning it up for printing.

I used software called DeVide, which no longer works in Windows, to do the initial job of isolating the tissues for a 3D printable model.  I also made multiple still images by sweeping the tissue density, then assembled them into an animated .gif file:

These days there are other software packages that can do the image processing, and it doesn't matter if the data is from a CT scan (x-ray based) or an MRI (magnetic, images water in tissues).  If you have a Mac, look up Osirix.  For windows there's InVesalius.  3DSlicer works in Windows, Mac, and Linux.  

YouTube has how-tos for extracting models from DiCom data files.  Here's one for InVesalius:

Human skulls have cartilage, lots of soft tissue, bones, teeth, and air spaces.  When you extract a model from a CT scan using tissue density to select teeth, you lose a lot of low density bone (eye sockets, sinuses, etc.).  When you reduce the tissue density to try to get the low density bone into the model, you also get the cartilage.  That sort of thing leads to a lot of clean-up to make the model printable.  If I remember right, I ended up using 4 different software packages to finally produce a printable model from the CT scan data.

Pencil and toothpick cups made from CT scan.

I also made keyfobs from the same file.  You can find the models here.

One of the difficulties with trying to do this sort of thing is the difficulty of obtaining detailed CT or MRI scan data.  That stuff is all protected by patient confidentiality laws- even if you strip the files of patient name, etc., the file data contains a likeness of the patient's face so it can be linked to that person.  Unless you use your own data, you'll have a hard time finding data that you can use to extract a human skull.  There are several data bases on line that contain data of human and animal scan data, but they are often limited for academic use only.  

I have put my own CT scan data in the form of a Dicom multifile on line.  You can download it here.

If you ever have a scan done, you might want to make arrangements in advance to get a copy of the complete data.  If you wait until months later and request a copy, there's a good chance that only part of the data will be available.  Even though it is your data, you may have to pay a small copying fee to obtain it.

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