Hey guys, in this video I want to talk about how to 3D print your brain if you have a
neuroimaging file that you want to print on a 3D printer. I'm going to try to keep this video as
short as possible but I want to include a lot of information and I also have some clips and videos
of my brain that I recently 3D printed and I'm going to put a bunch of links in the description
box so that people can get, you know, the programs that they need to download and you can also read
some tutorials, which I used to print my own brain. I'm gonna try to include a bunch of
information but also keep the video short. So let me first show you guys a video of my 3D printed
brain. Here is the video with me holding my brain. As you can see, I only printed half of it but in
this video I'll talk about how you can print your whole brain or half a brain if you want to print
half. That's the surface that--the inside is like the surface that was build upon so it's not I'm
anatomically accurate but yeah that's what it looks like. Okay so to begin the file that we're
going to get at the end is going to be a dot STL file. That's a file that some 3D printers
will accept directly. Freesurfer, which is a program that's free to download and to use for
neuroimaging, it's used a lot for pre-processing and statistical analysis of neuroimaging data
and it also has a function that lets you convert from your neuroimaging file to a STL file but we
don't want to convert the raw data, which would be like the DICOM or the NIFTIs, we first have
to do cortical reconstruction because we want to get the surface files, the files from the surface
folder. I'm going to assume you're starting with a DICOM or a NIFTI. If you're starting with a DICOM,
you want to convert it to a NIFTI. There's a program called DICOM2NIFTI converter. If you
guys have any questions or if I'm skipping any steps, just leave me a comment below and I'll
try to answer. But we're going to start with a NIFTI like this one. This is my brain. I'm going
to open a terminal window and I have cd'd into my desktop folder, which is where my NIFTI is.
To get the files from the surface folder, we're going to do recon-all. The steps for that is you
cd into the folder that has your NIFTI. Then we're going to do recon-all all. So the all flag says to
do the full reconstruction all the steps. You need the -s flag for the name of your subjects folder.
I just label it like that. And then you need -i for the input file. This is where you're going
to write the name of your NIFTI. And that's all the flags that you need. You can play around with
adding additional flags if you're familiar with freesurfer or if not that will start running. I'm
not going to click enter because I already have a subjects folder with this file already completed
but once that's done, it will print out a message saying it completed without errors on the terminal
and then you go to your free surfers subjects folder and you should have the subjects folder
created with a surface folder. So let me go ahead and pull that up because I've already done that.
Mine is in documents and then subjects and so this is the one that I ran a couple of days ago and
here is the surf folder that I'm talking about. If you do auto recon-all all, it will print all
these files for you and then you want to convert the pial files. Let me show you the two ways you
can either convert a whole brain or you can do it hemisphere by hemisphere. There is a function
that is in freesurfer called mris_convert. I think there used to be one called mri_convert
but I was testing it the other day on freesurfer 6 and they might have expired it because I think
you could just use mris_convert for one file or multiple files. I think that's like the primary
function now but anyway--Actually first let me go to the subjects folder. I cd'd into my surf
folder and this has all the dot pial extensions, which is what I want to convert. If you want to
do a whole brain and you want to 3D print that, then you do a flag called combine surfs. This will
combine multiple surfaces into one file and the two files are rh.pial and lh.pial. This obviously
stands for right hemisphere and left hemisphere. And then the last thing you want to input is the
name of the file. You can call that new cortex or something and the file extension is dot STL.
That will take like probably just a minute to run and the new file has been created. Something that
I've noticed, which I think might be like a bug in freesurfer 6 is I wanted to call it new cortex
but it saves the file name as lh.new cortex. You can obviously just go in and change the file name
but it seems to be picking up--I don't know why I adds lh even though I didn't write lh on there.
But anyway, the file is created and let me show you--so there's a free program that you can use
called meshlab. Let me show you what the file looks like so I can prove that it is indeed a
whole brain. Let me find the file again...where is it...This is the one we just created and if
we open it up, it shows you the whole brain. And so the left and the right have been combined and
let me also quickly show you guys what it looks like if you just do the left hemisphere or the
right hemisphere. I think I already have that done in that case. So let me just show you the
left hemisphere. This is the one that I printed, I printed my left hemisphere and the file itself has
the correct anatomy on the inside but it didn't print--I don't know enough about 3D printing to
know how you can get accurate--the base to be accurate as well because I think--I don't know
about that. But anyway that's how it would look if you just wanted to print one hemisphere like I
did, in which case you can again use mris_convert. You don't need to combine surf flags. You would
just do something like that and that will give you one of the hemispheres. You can literally just
print these files now. You can literally send them to a 3D printer. I printed these and my university
that has a whole lab and I had people help me who know about 3D printing. They just needed the STL
file but I saw online like some tutorials saying that you can do a couple alterations before you
send it to the printer. You can do that in mesh lab. That's the second part to this tutorial,
basically. Once you have the file, let me go find it again, you can simplify the number of
faces of the file, for example, and you can do a Laplacian transform and this is just done to
simplify the outer cortex. You can either do it or not, but if you simplify it it will make it faster
to print. The smaller and the simpler it is, it makes it easier to print and it also...what else
is there? I guess--well, it will also be cheaper, I guess that way. But you can decide for yourself
whether you want to do it or not but meshlab has options if you go to Filters. I read--and this is
mostly just based on tutorials I had read--someone did reduce the number of faces and you can do that
this way. If you reduce it to one hundred fifty thousand faces. Let me show you how that will
change the surface. Okay so if you can see, that kind of made it a little bit more of a smooth
surface. It reduced the complexity and you can also do a Laplacian transform, which again will
just smooth out the number of points. If you do it one time then you will have something that looks
like that. I think for me, since I only printed one hemisphere I didn't bother reducing the number
of faces but I did do a Laplacian transform before I sent it to the printer. Okay so those are the
main two parts. The third part of this video, I guess I wanted to share some photos and videos
that I took of while it was printing because, like I said, I printed this at a university lab
so I talked to some people who know about 3D printing and they gave me some advice. One of
the things they told me--and you can try to look up like a lot of public libraries nowadays even
have 3D printers or you can order your prints online or if you're a university student like
me you can probably find a 3D printer on campus. They--my university has a whole lab--they told me
for example to print it hemisphere by hemisphere because at first they were looking at printing it
whole and they just noticed that the base would not be very good. They basically were kind of
worried that if they printed it, the print would fail because there's a way of checking how many
points you have on a base and they told me it would be stilted, which could be bad for the
print. They suggested to me to split it hemisphere by hemisphere and print it like that and that
would be better for the base. And it printed just fine, so I guess they were right although I've
seen a lot of people online print the whole brain. So I'm sure there's a way of doing it as well and
you could probably try it even if it's stilted and maybe it would still work...What other suggestions
did they do? There's a program that they put into. I think it was called cura, c u r a, that
they--they input it into cura and then look at it and see how long it's going to take to print. For
me, they scaled. I--so I only printed half of my brain--so the left hemisphere--and they scaled it
to 50% and that took 4 hours, as you'll see in the photos. They also charged me by how many grams it
was and yeah, I think it was by grams. It's not necessarily by hours but obviously the bigger it
is, the longer it takes. What else did I want to say? Yeah, so that's kind of my explanation for
printing only half. Yeah and so you might want to consider like talking to people who know about 3D
printing to see what's the best way to print but this STL file is the standard that's used,
or one of the standards that's used for any 3D printer. And yeah, let me end the video now with
just showing some photos and videos of me in the lab and that'll be the end of this video.
*chiptune music*