Raspberry Pi meets Cognitive Neuroscience

Can the Raspberri Pi be used to process 4d neuroimaging data?

Can the Raspberri Pi be used to process 4d neuroimaging data?

When I started my masters degree, I didn’t entirely know what I was taking on. I chose to study cognitive neuroscience because I knew this was an area which presently receives a lot of funding for PhD research, and also because it seemed like a robust, scientific approach to psychology. After a few short months I have come to discover that research in this area is something that I really enjoy, and that is largely down to the opportunities to program and develop computerized research tools.

At the same time, the Raspberry Pi Foundation have announced and launched the new Raspberry Pi 2: a credit card sized motherboard which can be run as a standalone personal computer. I’m not going to go in to all the ins and outs of the Raspberry Pi (or Pi, for short), you can find more about it by visiting their website at www.raspberrypi.org. Instead, I want to talk about what it brings to the study of psychology.

Anybody who has studied psychology as a science will know that a lot of research is made up from undergraduate students sitting in dark rooms performing mundane tasks while their reaction times were being measured. This has been terrific for the creators of Matlab, whose IDE has facilitated many a psychology-button-pressing extravaganza. Even so, there is a new kid on the block who is gradually gathering momentum, and that is python.

One of the modules we undertook this spring semester was programming in python, something I hadn’t done before. I was keen to do at least some of this on the Pi, so as to justify my impulsive buying of it. My lecturer found kind of cute (that would be “cute”, except that he didn’t say it aloud). I persisted non the less, until I found that at least for graphics the Pi weren’t altogether compatible with the PsychoPy module we were using. Unfortunately it does not support Open GL graphics, so it actually struggles with button pressing experiments. But it was a start, it wet my appetite, and it was fun.

The real fun has commenced as I’ve begun my dissertation project. We’re doing some work on spatial cognition (how space is represented in the brain) using functional magnetic resonance imaging (fMRI), and part of this involves calculating different test statistics on 3d data on a voxel by voxel basis (voxel = volumetric pixel). There is lots of python modules optimized for flattening, analyzing and reassembling these datasets and we’re using them to build novel analyses which haven’t been done before. On this frontier of neuroimaging research, the raspberry pi stands gallant as my building platform and testing station to produce these scripts.

I’ve been using the module ‘minepy‘ to calculate the Maximal Information Coefficient (MIC) for each voxel in a set of datasets. The modules install seamlessly on the pi from the different repositories, and scripts can be written elegantly through the ‘spyder‘ IDE. I’m most excited most of all about the sheer size of the data we are working with. Each dataset is 64x64x26 voxels, which means 106496 calculations. On the Pi, each one takes about a second, and (when I close the GUI) all in all it takes about 2 hours. For me to run this on all 48 of our scans, that would take about 4 days. For processing the whole lot, fortunately we can pass our script to the cluster computer at York, which (assuming it is coded correctly) should polish it all up in around 16 hours.

It looks like something out of a movie, but its real!

It looks like something out of a movie, but its real!

What I really like about this is how real it all is. I’ve taken on many little projects here and there over my years, but none of them have ever really meant anything. Sure, I learned a lot, but I wanted to put it into action. Here, when those lines of text fly up my screen for 2 hours, I look forward to the output for reasons more than just knowing it worked. It also gives me the opportunity to work on my projects at home using a linux software environment, which great since Python runs natively in Linux.

This also ticks another box for the raspberry pi foundation. Universities and hospitals around the world have powerful workstations and supercomputers which they use to process neuroimaging data. That is very sensible, considering the sheer volumes they work with. But can it also be done on a £25 printed circuit board in Billy-whizz’s basement? Yes… It can!

Advertisements

A Word on Evolution

Evolution is a popular word within science these days, and psychology is no exception. It seems that just about everything, whether it be neuropsychology or developmental psychology, can link theories back to our so called evolutionary past.

And it does kind of fit. The regions of our brains that carry out more elemental (similar to animal) roles are all centred around the medulla, which becomes the spinal cord. The further you come from the medulla, the more executive functions are performed, which might suggest from the evolutionary standpoint that new bits were built around the older parts.

Today I was reading on vision, and it astounded me just how spectacular the visual system is. Now the notion of evolutionary psychology suggests that the elements of the visual system for the transduction of colour came later on, that certain parts of the visual system are colour blind, and that through additional pathways the colour information is sent, to make a picture in our ‘minds’.

I just cannot grasp how such a system could uniformly form across an entire species by chance. The scientific primary colours, which according to theory, out of mere chance have constructed into the cones of the visual system, them selves through accidental genetic mutation, I honestly believe to be impossible. With no complete set of systematic steps, something has made itself out of genes that once upon a time had no trace of colour information.

Many a scientist now do look at the spectacularity of nature and of the human body, and feel conviction that a power of deity is having a bigger role than science would be comfortable accepting. I myself am a firm believer in Jesus Christ, belonging to the Church of Jesus Christ of Latter-day Saints. Information and ideas such as what I refer to here play no part in my conversion to that faith – empirical evidence for such does not exist, but I do marvel at the hand of my creator in such a spectacular organism as the human brain.