This Fall semester, a sophomore-year Hopkins student Balaji Vijayakumar finished his interesting project – he made a 50%-size model of his actual brain on a 3D printer at the Digital Media Center in Homewood. How did he get this idea, why he decided to go with his project, how did this process look like, and what he going to do with this model – to learn more from his experience, Imagine talked to Balaji.
Balaji, you made a 3D model of your own brain. As a person who studies social science, I have to ask you – are we there already? Are we now ready to make models of our brains?
You know how MRIs [Magnetic resonance imaging] exist today, right? MRI gives you basically slices of your brain, like each layer. With those slices, there’s software that can merge them together, and by merging those slices together, you can get your whole brain. And if you put it to a 3D modeling software, it just takes the shell of that brain and a 3D printer can just print that shell. So, we are there, we do have the technology now.
How did you get this idea?
I always wanted to have some sort of image of my brain. I first learned about MRIs and wanted to do an MRI through these clinical trials that JHU does on their JHU hub. And I just wanted to do an MRI and was: “Oh that’s cool, I want to see how my brain looks.” So, I signed up for one of those clinical trials and in this one, they were just taking images of people’s brains for, I guess, for physical models that they were trying to do themselves. So I was like: “OK, I might as well do the clinical trial”
While signing up, I was actually in my lab and there my postdoc was overseeing my work. I told her about this, and she was like: “Oh yeah, so back in my college what they used to do is do MRIs and they took that, and they made like 3D brains with that.” So, it was actually my postdoc’s idea on how this is possible, and I was like: “Oh, that’s pretty cool.” She didn’t know necessarily how that was done because their university did it themselves, so I had to go figure out if this was even possible? Like, can I do this myself? And I had to figure out what software was needed and so on, but eventually I got it to work.
The DMC [JHU Digital Media Center] had the 3D printing technology, I needed somewhere to 3D print it. I didn’t really trust online services and there’s not anywhere else nearby that would do 3D printing, and there’s no trust in that either. I learned about the DMC this way too. I was looking if students have access to 3D printing themselves and I found that the DMC does, but they weren’t open back then, so I just waited until they were open and then I started doing it.
Did you know?
Johns Hopkins Digital Media Center is a one-stop-shop for all your media projects
Was it free to use?
There’s a charge for how long you 3D print, but other than that, yes.
How long did it take to complete this project?
The MRI took a while, it was like 4 hours. You’re just like sitting in the MRI. That was surprising for me. But the DMC wasn’t open back then. I did the MRI, I think, over the summer and the DMC wasn’t open until the beginning of this semester, so it was put on hold. And over the summer I was figuring out how to get that model already and so on. Once I had the model ready, I waited until the DMC was open and then I talked to Jason [Charney] about it and they actually bought a new printer so he was trying to get that set up, and he was like: “Yeah, you can print this, we’ll have like a day set up for it.” I didn’t print the whole size because if I was to print my brain full-size, it would take like 8 days to print at that detail. So instead, I printed it at like 50% size and so that itself was like 2 days. So he was trying to find a time where I could do it for 2 days continuously without disturbing anyone in the sense. So then after that, it took a month to get a perfect date and then it only took two days to print.
Now I feel much more comfortable 3D printing. I’m not an expert now, I’ve only done one project but I know that just enough to do other things. 3D printing, it’s not only just for fun, you can do it for these creative projects, but you can also create prototypes and so on. So with that skill, I guess I can use that in daily applications in a sense. It actually didn’t take that long. I guess back in the day, you have to put a lot of manual input in. But now once you get your 3D model, there are filters you have to apply onto it that make it more clean and then after that, once you put it into the actual 3D printing software, it takes care of it, and there’s only like oh, which size do you want it? And all those nitty gritty stuff that once you get fine, it’s basically automatic.
When I did the MRI, I had to ask them if it was OK if I used some of the files? And basically how MRIs are done, it’s something called a DICOM, and DICOM, it is basically just a series of code, but it’s more like each slice is an image. So then there’s another software called Freesurfer, and Freesurfer is what doctors use themselves to do the same thing of creating a 3D model. And what that does is combine all the images together and then I use that and that was honestly like a whole adventure in itself, because I have a Macbook and you know how many softwares don’t work on Macbook? So to get that to work and so on. Eventually I got it to work. Then Freesurfer itself creates a shell of the brain, so I took that and then I put into a 3D software like Meshlab or the machine printing software itself. And when you put it in there it can create all the supports, so it slices it again for the 3D-printer to know how to 3D print it. And that’s basically the whole process.
Do you use this model in your studies now?
Originally, I was just like: “Oh, this is just cool to have,” right? It’s like a showcase kind of thing like this is my brain, I can keep it, I can look at it. But I’m a Neuroscience major myself so as I continue learning about neuroscience, I can look at my own brain and I can be like: “Oh these parts relate to those parts.” I can actually see different features of my brain and actually understand why those exist. So in a sense, it’s like a model for me to look at like myself, and that also helps. This is kind of funny – another postdoc in my lab was looking at it and said: “Oh you have good grooves and that means you don’t have Alzheimer’s.”
Where are you in your program right now?
I’m a sophomore. I’m double majoring in neuroscience and molecular and cellular biology. I’m from St. Louis, I’ve basically been in St. Louis my whole time. We didn’t really come back to university until the spring of freshman year [Spring 2021 semester] and even in the spring of freshman year, we had restrictions. Over the summer I stayed here for doing research and then the Fall of sophomore year was when everything actually started going full in-person.
In 2020, we didn’t go to campus. I was still at home in St. Louis, so everything was online. Which was a change, I’m more used to in-person classes, that’s how I learn better and so on. So with online, it required changing how I study because I had to schedule myself. Most of these classes were asynchronous, so I had to make my own schedule and stick to that schedule but eventually, I got the hang of it. But other than that, since it’s online, there are not really fun activities, where you can meet other people and so on. So it’s more focused on just studies.
Do you plan any other projects like that?
Next semester, honestly, as things open up more and more opportunities come so I’m just waiting to see what’s open. I know Johns Hopkins has a lot to offer so as semester goes on, I would love to see what they have to offer and see where I can use those opportunities. I never knew how to 3D print, so this was like my first. I actually learned how to 3D print from Jason, Jason taught me how to do it. I don’t know how to use like half the resources in the DMC. There are many new things, like I don’t know how to do imaging, stuff like Photoshop and so on. So honestly, there’s a lot of resources that the DMC has to offer. I would just have to think of an idea and then take it there. One of my friends wanted to start a podcast with me so maybe using one of their audio resources or learning how to do that would be cool and something I might do in the future.