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rejiggering

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Cadey Ratio 2019-08-23 13:18:28 -04:00
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blog/brain-fmri-to-3d-model-2019-08-23.markdown
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@ -39,13 +39,15 @@ $ source env/bin/activate
(env) $ python3 setup.py install
```
Then I ran it with the following settings to get this first result:
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 src="/static/blog/christine-frmi-raw.mp4">A sideways view of the brain</video></center>
<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
@ -66,10 +68,12 @@ $ 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
I reran gif\_your\_nifti on this reoriented file and got [this result][secondgif]
which looked a _lot_ better:
<center><video src="/static/blog/christine-fmri-reoriented.mp4">A properly reoriented brain</video></center>
<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
@ -140,8 +144,8 @@ things I've ever done (if not the coolest) and I'm going to be able to get a
[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]: https://xena.greedo.xeserv.us/files/christine_brain_plasma.gif
[secondgif]: https://xena.greedo.xeserv.us/files/christine_brain_reoriented_plasma.gif
[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