Category Archives: Short Posts

Restarting Cinnamon after freeze without losing session information

August 28, 2015 nouyang 1 Comment

Whoo! For some reason, cinnamon freezes extremely often (multiple times a day) on my desktop, and I had been resorting to “ctrl-alt-f1” to get to a terminal and running “killall cinnamon-session”, which brings me back to login screen. Fortunately, there is a better solution, aka “ctrl-alt-esc”.

Here’s the relevant excerpt from the Cinnamon blog (http://segfault.linuxmint.com/2015/06/cinnamon-2-6/):

Desktop freezes

In case of a freeze or if you need to restart Cinnamon for any reason, you can now do so via a keyboard shortcut. The default key combination is Ctrl+Alt+Escape. Pressing this combination of keys restarts nemo and cinnamon-settings-daemon in case they had crashed, and launches a brand new instance of the Cinnamon desktop. Unlike Ctrl+Alt+Backspace which terminates your session and brings you back to the login screen, Ctrl+Alt+Escape simply restarts Cinnamon itself, which means your session is exactly as it was, you don’t lose any work and all your windows and applications remain open.

Gender, Short Posts

hack4fem: hack for feminism (conference & hackathon) logo

August 14, 2015 nouyang 1 Comment

I made a logo for a new project I am starting up. It’s a mashup of a bunch of openclipart files, It combines the feminist logo (fist inside Venus sign) with STEM (wrench for mechanical engineering / hands-on, lightning for electrical engineering, then on the nails, a graph for mathematics, beaker for science, and “</>” for coding). The logo expresses my desire to combine my STEM skills with my feminist / activist passions. I refuse to choose between activism and advancing my technical prowess.

Here is the SVG source, which I release back into the public domain.

If you’re interested in helping organize the first hack4fem conference, email me! 🙂 It’s set for Nov. 7th & 8th (Sat. and Sun.), 2015, in Boston, MA.

website, work-in-progress: hack4fem.org
slack: http://hack4fem.slack.com/

Short Posts

A gif of my brain (MRI scans)

July 22, 2015 nouyang 4 Comments

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

Turn all the DICOM files into single-image gif files
http://manpages.ubuntu.com/manpages/raring/man1/medcon.1.html
```
medcon -f * 2 -c gif acr intf
```
https://www.tjhsst.edu/~dhyatt/supercomp/n401a.html
```
convert -delay 5 -loop 0 m*.gif anim.gif
```

Then, upload to gfycat.

Other viewers

Mango

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

http://ric.uthscsa.edu/mango/mango.html

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:

file:///home/nrw/Pictures/ivmartel-dwv-2b340ec/viewers/static/index.html

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.

 <iframe width="512" height="512" style="-webkit-backface-visibility: hidden; -webkit-transform: scale(2); -webkit-transform-origin: 0 0; -moz-transform-scale(2); -moz-transform-origin: 0 0;" src="http://gfycat.com/ifr/BetterPhysicalIvorybilledwoodpecker" frameborder="0" scrolling="no"></iframe>

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.

orange narwhals