If you’re interested, we can give you a CD with a copy of all the data from the MRI after the procedure. I guess you could use it for…something? Wait, why do you want it?

Holding a 3D printed replica of my own brainHolding a full size 3D printed replica of my own brain

Living in the future is pretty cool, right? After scheduling my brain MRI, I was told that I would be given a CD with a copy of all of the data collected from the procedure. I don’t really know how to interpret it, but I figured I’d be able to at least make a 3D printed model out of it.

IMG_1550Unfortunately, no pictures were allowed inside the MRI room

Once at the hospital, I was told I wouldn’t be able to bring my camera into the room with me. The technologist informed me the machine I would be scanned with was the Siemens Magnetom Sonata. The process took about an hour, most of which was spent in the tube. I had my eyes closed for the duration; I’ve simply read too much Poe to even think about trying to look around while stuck in that tube.

This is the same machine that I was scanned inThis is the machine that I was scanned in

Downloading the Software

You’ll need Blender, netfabb, and OsiriX (Mac-only software). Blender can be substituted for any CAD program, but Blender is the easiest for me to work with (I’m slowly graduating from TinkerCAD!). In addition, OsiriX is OS X only, but there are other free and open-source DICOM viewers for PC.

Editing the Model

The CD contained about a dozen different scans of my brain. Each scan was focused on a different part of my brain, so each was missing a different part. Some were missing large pieces of the sides, some were missing the top, etc. I picked the best scan of the group, which was the only one that had all of the brain captured.

The scan!A 360 degree view of the scan

The model still requires a good bit of adjusting in OsiriX, as you want to isolate the brain while removing the skull, skin, and eyes. Easier said than done; this process took me about an hour.

The model in OsiriXThe model in OsiriX

Once finished, I exported the .STL and checked it in NetFabb. Everything looked solid, so it was time to start the clean-up.

The model directly after being exportedThe model directly after being exported

Using Blender, I cleaned up the floating bits of skull and removed the eyes and various bits of muscle that weren’t actually part of the brain. There was a lot of skull that was attached to the base of the brain that needed to be removed, and it was delicate, time-consuming work.

The orange bits are highlighted and removed. This process is lengthy and unrewarding.The orange bits are highlighted and removed. This process is lengthy and unrewarding.

After the cleanup, there were a few holes in the bottom of the brain. Talented 3D illustrator and artist Cindy Raggo finalized the model and created the finished product.

The cleaned up version before printing.The cleaned up version before printing.

Printing the Model

The model was printed on an UP! Box (or Afinia H800) printer at 3D Central in Richmond, VA. I printed it at medium-low resolution (.2 mm), so it would print in a reasonably short period of time. At full-size, it still took 49 hours to print!







If you get an MRI, I highly suggest taking the free copy of the data. While the software available is still not quite to the point where it is easy to interpret and use for the average user, in the next few years, I think it will be. The data you have will last a lifetime, and you’ll be glad you saved it.


Need more info? Want to know about the process? Have you tried this method before but got a different result? Shoot me an email at andrew@sinkhacks.com or https://twitter.com/AndrewASink.

Software used:

OsiriX: http://www.osirix-viewer.com/
Blender: https://www.blender.org/
Netfabb: http://www.netfabb.com/

3D Modeling Assistance:

Cindy Raggo : cindy-raggo.squarespace.com

Download: http://www.thingiverse.com/thing:1287025