A gif of my brain (MRI scans)

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http://www.gfycat.com/BetterPhysicalIvorybilledwoodpecker

(License: Public Domain, https://creativecommons.org/publicdomain/zero/1.0/)

I participated in a research study last night and got a CD with 40 MB of scans of my brain. Yay!

I didn’t have a fancy DICOM viewer like OSIRIx, which lets you fly through the brain in any direction you want by reconstructing the data appropriately from the MRI slices, but I was able to make the above gif using just two lines on the command-line in linux.

How I made the gif

Then, upload to gfycat.

Other viewers

Mango

A DICOM viewer (kind of clunky / not well integrated into Ubuntu):

DICOM Web Viewer

A browser-based DICOM viewer that is somehow better integrated into linux:

https://github.com/ivmartel/dwv

To use, download and unzip, go to the folder for the viewer you want, and open up “index.html”. For instance:

Then click “file” and select all the files you want to open.

Scaling Gfycats (in embedded iframes)

The gfycat was pretty small, so I wanted to embed a scaled-up version here. Doing so took me a few minutes to figure out, so here it is. After getting the iframe code from gfycat.com, I manually set the width and height to be 2x, then set scale to be 2  and added scaling for firefox.

However, my image was now scaling off the page! From stackoverflow I figured out that I need to add “transform-origin” attributes in there. See below.

Update: 29 July 2015

I found a better viewer than mango and dwv. Slicer lets you see the brain scans from any angle (the defaut is top – side – back), and you can import ALL the DICOM files and it will sort out for you which ones belong to a “series” (hard to do in the native file manager since my file manager doesn’t show DICOM previews). See pictures below.

To get slicer, go to http://download.slicer.org/ and download the .tar.gz, then extract its contents. Go into the extracted root folder (something like “Slicer-4.4.0-linux-amd64”) and run the executable in the root folder.

Screenshot from 2015-07-28 19:46:04

Screenshot from 2015-07-29 04:43:05

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