Day 8

It's been a while since I've posted. I wasn't at the lab on Thursday and Friday, but Spiro gave me the script to work on over the weekend. I'm going to try and explain what this script does and what I did today, but if it doesn't make sense please leave a comment or something so I can clear it up. I believe I have to present it to some people on Thursday.
I'll start by explaining Spiro's work. Spiro is researching graph theory in neuroscience. Basically, the whole brain is connected in two ways: physical connections and functional connections. Using DTI (mentioned in previous posts) we can easily map physical connections, and using fMRI we can map functional connections. Spiro is using both DTI and fMRI to map the connections between certain areas of the brain during fear responses. (Side note: Fear is very commonly studied in neuroscience labs. The brain and body react to fear in many quantifiable ways, so it is nice to use for mapping certain connections in the brain. Often, studies are done with people with and without high anxiety or anxiety disorders, because they have different pathways for fear.) In his research, Spiro has acquired data on how many connections certain "nodes" of the brain have at both baseline and during fear responses. (A node is part of a large structure of the brain. There are normally four nodes in each known structure.) The point of this script is to put all the data from these nodes and put them onto the same brain. Each node is recorded on an image. That image has values (called "Intensity Values") at every point (voxel) on the brain, however, not all of the points matter. The first thing that this script does, is set every voxel below a certain intensity (defined in the script) to zero. Next, it sets every value above zero to be one. These two steps create an image that highlights only the node, with one value in each highlighted voxel. The script then multiplies every value in the image by the number of connections (defined by a vector the user inputs). The script repeats these steps for all 369 nodes, adding each one to a final image. Finally, that image is overlaid onto a standardized brain. (Did that make sense?)
Today, I took the script, which initially took 4 minutes, 40 seconds to run, and sped it up to take only 2:18. I did that by combining a few steps that created temporary images for each step. By not creating and deleting images on each step, the script runs much faster. I also made it so that the script automatically opens up the image (color-coded) once it finishes running. Finally, I added in the ability to choose your own threshold value (the number below which all values turn to zero). It took me easily a half hour to figure out how to input the threshold value. The script is now done, which is awesome!

Today we also saw one of the post docs present her research. Her presentation was about an hour long, and was a bout fear connections in mice. It was an extremely interesting talk. She was doing a practice talk for her job interview, which is tomorrow.

Tomorrow I may begin to figure out what I am going to work on for the rest of the summer. Woo hoo!