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How I Converted my Brain fMRI to a 3D Model

AUTHOR’S NOTE: I just want to start this out by saying I am not an expert, and nothing in this blogpost should be construed as medical advice. I just wanted to see what kind of pretty pictures I could get out of an fMRI data file.

So this week I flew out to Stanford to participate in a study that involved a fMRI of my brain while I was doing some things. I asked for (and recieved) a data file from the fMRI so I could play with it and possibly 3D print it. This blogpost is the record of my journey through various software to get a fully usable 3D model out of the fMRI data file.

The Data File

I was given christine_brain.nii.gz by the researcher who was operating the fMRI. I looked around for some software to convert it to a 3D model and /r/3dprinting suggested the use of FreeSurfer to generate a 3D model. I downloaded and installed the software then started to look for something I could do in the meantime, as this was going to take something on the order of 8 hours to process.

An Animated GIF

I started looking for the file format on the internet by googling “nii.gz brain image” and I stumbled across a program called gif_your_nifti. It looked to be mostly pure python so I created a virtualenv and installed it in there:

$ git clone https://github.com/miykael/gif_your_nifti
$ cd gif_your_nifti
$ virtualenv -p python3 env
$ source env/bin/activate
(env) $ pip3 install -r requirements.txt
(env) $ python3 setup.py install

Then I ran it with the following settings to get this first result:

(env) $ gif_your_nifti christine_brain.nii.gz --mode pseudocolor --cmap plasma

(sorry the video embed isn’t working in safari)

It looked weird though, that’s because the fMRI scanner I used has a different rotation to what’s considered “normal”. The gif_your_nifti repo mentioned a program called fslreorient2std to reorient the fMRI image, so I set out to install and run it.

FSL

After some googling, I found FSL’s website which included an installer script and required registration.

37 gigabytes of downloads and data later, I had the entire FSL suite installed to a server of mine and ran the conversion command:

$ fslreorient2std christine_brain.nii.gz christine_brain_reoriented.nii.gz

This produced a slightly smaller reoriented file.

I reran gif_your_nifti on this reoriented file and got this result which looked a lot better:

(sorry again the video embed isn’t working in safari)

FreeSurfer

By this time I had gotten back home and FreeSurfer was done installing, so I registered for it (god bless the institution of None) and put its license key in the place it expected. I copied the reoriented data file to my Mac and then set up a SUBJECTS_DIR and had it start running the numbers and extracting the brain surfaces:

$ cd ~/tmp
$ mkdir -p brain/subjects
$ cd brain
$ export SUBJECTS_DIR=$(pwd)/subjects
$ recon-all -i /path/to/christine_brain_reoriented.nii.gz -s christine -all

This step took 8 hours. Once I was done I had a bunch of data in $SUBJECTS_DIR/christine. I opened my shell to that folder and went into the surf subfolder:

$ mris_convert lh.pial lh.pial.stl
$ mris_convert rh.pial rh.pial.stl

Now I had standard stl files that I could stick into Blender.

Blender

Importing the stl files was really easy. I clicked on File, then Import, then Stl. After guiding the browser to the subjects directory and finding the STL files, I got a view that looked something like this:

I had absolutely no idea what to do from here in Blender, so I exported the whole thing to a stl file and sent it to a coworker for 3D printing (he said it was going to be “the coolest thing he’s ever printed”).

I also exported an Unreal Engine 4 compatible model and sent it to a friend of mine that does hobbyist game development. A few hours later I got this back:

(Hint: it is a take on the famous galaxy brain memes)

Conclusion

Overall, this was fun! I got to play with many gigabytes of software that ran my most powerful machine at full blast for 8 hours, I made a fully printable 3D model out of it and I have some future plans for importing this data into Minecraft (the NIFTI .nii.gz format has a limit of 256 layers).

I’ll be sure to write more about this in the future!

Citations

Here are my citations in BibTex format.

Special thanks goes to Michael Lifshitz for organizing the study that I participated in that got me this fMRI data file. It was one of the coolest things I’ve ever done (if not the coolest) and I’m going to be able to get a 3D printed model of my brain out of it.


This article was posted on 2019-08-23. Facts and circumstances may have changed since publication. Please contact me before jumping to conclusions if something seems wrong or unclear.

Series: howto

Tags: #python #blender