diff --git a/blog/brain-fmri-to-3d-model-2019-08-23.markdown b/blog/brain-fmri-to-3d-model-2019-08-23.markdown index 74e6a8a..545e665 100644 --- a/blog/brain-fmri-to-3d-model-2019-08-23.markdown +++ b/blog/brain-fmri-to-3d-model-2019-08-23.markdown @@ -1,14 +1,13 @@ --- -title: How to Convert a Brain fMRI to a 3D Model +title: How I Converted my Brain fMRI to a 3D Model date: 2019-08-23 --- -# How to Convert a Brain fMRI to a 3D Model +# How I Converted my Brain fMRI to a 3D Model -AUTHOR'S NOTE: I just want to start this out by saying I do not know what I am -doing here. I am not an expert, 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. +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 @@ -40,12 +39,14 @@ $ source env/bin/activate (env) $ python3 setup.py install ``` -Then I ran it with the following settings to get [this first result (30 MB)][firstgif]. +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 ``` +
+ 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 @@ -63,10 +64,12 @@ 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] +This produced a slightly smaller [reoriented file][secondniifile]. -I reran gif\_your\_nifti on this reoriented file and got [this result (30 MB)][secondgif] -which looked a _lot_ better. +I reran gif\_your\_nifti on this reoriented file and got this result +which looked a _lot_ better: + +
### FreeSurfer @@ -103,7 +106,7 @@ files, I got a view that looked something like this:

BRAIN pic.twitter.com/kGSrPj0kgP

— Cadey Ratio 🌐 (@theprincessxena) August 22, 2019
-I have absolutely no idea what to do from here in Blender, so I exported the +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"). diff --git a/static/blog/christine-fmri-raw.mp4 b/static/blog/christine-fmri-raw.mp4 new file mode 100644 index 0000000..94d98be Binary files /dev/null and b/static/blog/christine-fmri-raw.mp4 differ diff --git a/static/blog/christine-fmri-reoriented.mp4 b/static/blog/christine-fmri-reoriented.mp4 new file mode 100644 index 0000000..63dae26 Binary files /dev/null and b/static/blog/christine-fmri-reoriented.mp4 differ