forked from cadey/xesite
153 lines
6.6 KiB
Markdown
153 lines
6.6 KiB
Markdown
---
|
|
title: How I Converted my Brain fMRI to a 3D Model
|
|
date: 2019-08-23
|
|
---
|
|
|
|
# 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][firstniifile] by the researcher who was
|
|
operating the fMRI. I looked around for some software to convert it to a 3D
|
|
model and [/r/3dprinting][r3dprinting] suggested the use of [FreeSurfer][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][gyn]. 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][firstgif]:
|
|
|
|
```
|
|
(env) $ gif_your_nifti christine_brain.nii.gz --mode pseudocolor --cmap plasma
|
|
```
|
|
|
|
<center><video controls> <source src="https://xena.greedo.xeserv.us/files/christine-fmri-raw.mp4" type="video/mp4">A sideways view of the brain</video></center>
|
|
|
|
<small>(sorry the video embed isn't working in safari)</small>
|
|
|
|
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][fsl] 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][secondniifile].
|
|
|
|
I reran gif\_your\_nifti on this reoriented file and got [this result][secondgif]
|
|
which looked a _lot_ better:
|
|
|
|
<center><video controls> <source src="https://xena.greedo.xeserv.us/files/christine-fmri-reoriented.mp4">A properly reoriented brain</video></center>
|
|
|
|
<small>(sorry again the video embed isn't working in safari)</small>
|
|
|
|
### FreeSurfer
|
|
|
|
By this time I had gotten back home and [FreeSurfer][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].
|
|
|
|
### 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:
|
|
|
|
<center><blockquote class="twitter-tweet"><p lang="en" dir="ltr">BRAIN <a href="https://t.co/kGSrPj0kgP">pic.twitter.com/kGSrPj0kgP</a></p>— Cadey Ratio 🌐 (@theprincessxena) <a href="https://twitter.com/theprincessxena/status/1164526098526478336?ref_src=twsrc%5Etfw">August 22, 2019</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script></center>
|
|
|
|
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:
|
|
|
|
<center><blockquote class="twitter-tweet"><p lang="und" dir="ltr"><a href="https://t.co/fXnwnSpMry">pic.twitter.com/fXnwnSpMry</a></p>— Cadey Ratio 🌐 (@theprincessxena) <a href="https://twitter.com/theprincessxena/status/1164714830630203393?ref_src=twsrc%5Etfw">August 23, 2019</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script></center>
|
|
|
|
(Hint: it is a take on the famous [galaxy brain memes][galaxybrain])
|
|
|
|
## 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][citations].
|
|
|
|
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.
|
|
|
|
[firstniifile]: https://xena.greedo.xeserv.us/files/christine_brain.nii.gz
|
|
[secondniifile]: https://xena.greedo.xeserv.us/files/christine_brain_reoriented.nii.gz
|
|
[r3dprinting]: https://www.reddit.com/r/3Dprinting/comments/2w0zxx/magnetic_resonance_image_nii_to_stl/
|
|
[freesurfer]: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
|
|
[gyn]: https://github.com/miykael/gif_your_nifti
|
|
[firstgif]: /static/blog/christine-fmri-raw.mp4
|
|
[secondgif]: /static/blog/christine-fmri-reoriented.mp4
|
|
[fsl]: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/
|
|
[blender]: https://www.blender.org
|
|
[galaxybrain]: https://knowyourmeme.com/memes/expanding-brain
|
|
[citations]: /static/blog/brainfmri-to-3d-model.bib
|