The most complicated and fascinating gadget you will ever own is your brain. Why not pay tribute to this wonder by creating a 3D scale model that you can print yourself? If you have had a full-head MRI scan, it is simple to take this data and create a 3D model that you can print out on any 3D printer. Here’s how to print your brain.
To begin, you are going to need an MRI scan. Unfortunately, the low-field MRI that [Peter Jansen] is working on won’t quite cut it (yet): you’ll have to get the pros to do it. The type of scan also matters, because we want a scan that focusses in on the brain itself, not the bits around it. What type you get depends on what your doctor wants to know, as the radiologist can run a lot of different scans and analysis of the data to show different types of tissue. After looking through the scans that I got, I settled on one that was labelled eB1000i(BRAIN) With and Without Contrast. To a radiologist, that information means a lot, telling you what type of scan it is, and that it was done with a contrast agent, a metal dye that is injected to make water-rich tissues (like my brain) more visible. The number refers to something called the diffusion weighting, which helps the doctor look for swelling that can indicate things like strokes, tumors, etc. There’s a good guide to some of the jargon here.
Request your DICOM Data
If you are having an MRI, you can request a CD immediately after the scan, or contact your doctor: as a patient, you have a right to a copy of this data. You’ll receive a CD that includes the MRI images in a format called DICOM. Short for Digital Images and Communications in Medicine, this is an open format that is used by most medical systems. The CD will include a Windows program that allows you to view these files, which is worth checking out, as scrolling through your own brain is a rather surreal experience. If you haven’t had an MRI, there are a lot of sample scans available that you can use. Osirix offers a few of the brain (and other bits), and there are a number of scans available here.
Magnetic Resonance Imaging is a fascinating bit of science where a very strong magnetic field is used to excite the water atoms in your body. After the hydrogen atoms in these molecules are excited by this field, they emit a radio signal, which the MRI machine detects. By shaping the magnetic field, the MRI gradually maps the brain, figuring out which tissues have lots of water (such as blood vessels) and which have less, such as bone. The device gradually combines this info into images of your insides without having to actually get in there and poke them. If you are interested in the physics and mathematics of this process, there is an in-depth guide here.
To process and convert these images, there are several free and open source programs available, such as Slicerweb, Osirix, 3DSlicer and Invesialus. These all have their own pros and cons, but I’m going to use Invesalius in this tutorial, as it is the easiest to work with and is available for windows, mac and Linux.
Your Brain in Software
Once you have installed the program, open it and select Import DICOM Images. If you had several different series of scans done, you can load them all at once: just select the top level directory of the CD, and the program will go into each directory and sort them so you can select the best scan. After it loads the files, it will show you previews of each scan. Choose the one that shows the brain the clearest, with as little of the rest of you as possible. To load these images for analysis, select import.
This will load the scan images, and show you four windows. Three of these are views (or slices, as the pros call them) through your head from different angles: from the top (Axial), the side (Sagittal) and the front(Coronal). The fourth will be blank at the moment: that is where the 3D model will show up. You can scan through the images for each view using the scroll bars on the side of the window.
Next, we are going to pick out the bits we are interested in. This is done using a mask, where you pick the good bits and discard the rest. This mask works like a narrowpass filter: you can create a narrow band of stuff you want, and disregard the rest. On the left is a window with a slider in it. When you change the upper and lower boundaries of this slider, you will see that the selected area of the scan (shown in green) changes. You want to set this so that as much of the brain is selected and as little of everything else. The program does offer a number of presets for different types of tissue from the drop-down menu, but I found that the custom preset was more effective. Again, you can scroll through the images using the scroll bar to the left of each window to see how the different slices are being masked. If you are having problems making a clean mask, click on manual edition and use the erase brush to get rid of the bits that are not brain.
When you are done, hit the create surface button. After some pondering, the program will create the 3D surface from the masks and show it in the fourth window. Don’t worry if there are some odd bits that aren’t brain: we’ll get rid of these later. To spin the surface, click and hold on the left mouse button. If you are happy with this surface, click on Next Step and select Export 3D surface. Save this surface as a .STL file.
We now have an STL file. However, it isn’t ready for printing yet. Next, we are going to use MeshLab to clean the model up and getting it ready for printing. Run MeshLab and load the STL file with File>Import Mesh. MeshLab will allow us to remove the bits of the model we don’t need. I found that the easiest way to do this was to spin the model around and use the Select Faces In a Rectangular Area and the Delete Points, Verticies and Faces tool to remove the bits we don’t need. MeshLab uses a lot of memory when processing complex models like this, so don’t be surprised if it is unresponsive. If you are really struggling, try a filter that reduces the number of faces on the model, such as Filters>Remeshing, Simplification and Remodelling>Quadric Edge Collapse Decimation. Be careful, though: too much filtering will remove the detail from the model, which is what we are after.
Once you have removed all of the extraneous parts of the model, select Filter>Remeshing, Simplification and Remodelling>Close Holes. This will seal any holes in the model and get it ready for printing.
Finally, select File>Export Mesh and save the file as an STL file. Now, you are ready to load the model for printing! Any 3D printing program should be able to load the program and process it for printing out. I printed mine using Cura on a TAZ 5 printer.
3D Printing Your Brain
I was quite pleased with how my print turned out. The convoluted texture of my grey matter was well captured and printed on the top of the brain, but the similar texture on the side wasn’t quite as clear. That’s probably because of the way the scan was processed. I could get more detail on the side by using other scans and combining the results.
Now I have the 3D model, the possibilities are endless. I could print it in flexible plastic to give my cats an amusing toy. I could laser-cut it out in wood to produce an interesting ornament. Or I could do a small print to have available the next time someone asks to speak to the brains of this organization….