Friday, October 4, 2013

Multi-Variate Pattern Analysis (MVPA): An Introduction

Alert reader and fellow brain enthusiast Keith Bartley loves MVPA, and he's not ashamed to admit it. In fact, he loves MVPA so much that he was willing to share what he knows with all of us, as well as a couple of MVPA libraries he has ported from Matlab to Octave.

Why don't I write a post on MVPA, you ask? Maybe because I don't know doodley-squat about it, and maybe because I'm man enough to admit what I don't know. In my salad days when I was green in judgment I used to believe that I needed to know everything; nowadays, I get people to do that for me. This leaves me more time for gentlemanly activities, such as hunting, riding, shooting, fishing, and wenching.

So without further delay, here it is: An introduction to MVPA for those who are curious about it and maybe even want to do it themselves, but aren't exactly sure where to start. Be sure to check out the links at the end of the post for links to Keith's work, as well as Octave distributions he has been working on.


Well, it had to happen sometime. Time to call out the posers. Those who would bend neuroscience to their evil will. Where to start? How about the New York Times. Oh, New York Times. You've managed to play both sides of this coin equally well. Creating a neuroimaging fallout with bad reports, then throwing out neuroscience studies altogether ("The brain is not the mind" <- What? Stop. Wait, who are you again? Just stop). What's to be said for those few that rise above the absolutes of "newspaper neuroscience", and simply report findings, not headline grabbing inferences? Should we be opposed to gained knowledge, or seek to better understand the details? Boring you say? Pfft. Then you have yet to know the neuroscience I know.

As an example, a recent NYT article suggested that activation in both the primary auditory and visual cortices in response to an iPhone ring alone demonstrated that people were seeing the iPhone in their mind's eye.

This is a completely RIDICULOUS notion to suggest from univariate GLM BOLD response alone. But can we ever really know what a person sees in their mind's eye or hears in their mind's ear? Remember, good science happens in the setup, not the interpretation.

You may have heard of an increasingly implemented form of machine classification in brain-imaging dubbed Multi-Variate Pattern Analysis (MVPA). If you prefer the term "mind reading", sure go ahead, but remember to bring your scientific floaties, lest you drown from the lack of understanding as it escapes the proverbial lungs of your deoxygenated mind. Before you know it, you'll be believing things like this:

Verbose laughter ensues. Close, but no Vicodin. How does MVPA of BOLD responses really work?

Source: Kaplan & Meyer, 2011

By first training a program to recognize a pattern, in much the same way you might visually recognize a pattern, we can quantitatively measure the similarity or dissimilarity of patterns in response to differing conditions. But what does this have to do with knowing what a person might see in their mind? I recently compiled some soundless videos for a demonstration of just this. Watch them fullscreen for the greatest effect.

It's likely that the sound of coins clanking, a car crashing, or Captain Kirk screaming "KAHHHHN!!!" registered in your mind, and thus created distinct neural representations in your primary auditory cortex. If we train a machine classifier to recognize your brain's patterned neural response to the sound, we can then ask the classifier to guess which among all these stimuli your brain is distinctly representing in the absence of sound. If the machine classifier is successful statistically more than null permutations of chance, THEN we can MAYBE begin to suggest a top-down neural mechanism of alternate sensory modality stimulation. 

BUT, I promised you details, and details you shall have!

As a fan of Princeton's MVPA Matlab toolbox, opening it up for people without access to a Matlab license seemed like the next most logical step, prompting me to convert the toolbox, as well as its implementations of SPM and AFNI-for-MATLAB, to one unitary Octave distribution. Below is a link to my website and Github page. There you will find setup instructions as well as tutorial data and a script that Dr. Marc Coutanche (See his rigorously awesome research in MVPA here) and I implemented in a recent workshop. Coded are step-by-step instructions to complete what is a research caliber implementation of pattern analysis. Learn it, live it, repeat it, and finally bask in your ability to understand something that would make your grandma's head explode (See the Flynn Effect for possible explanation there). As with anything I post, if you have questions, comments, or criticisms, feel free to message me through any medium of communication ...unless you are a psychic. I'd like to keep my mind's ear to myself. 


  1. Hey Andrew, love the MVPA walkthrough. I'm glad to see you back posting frequently again as a relative newbie to image analysis

    1. Hey John, glad you like it! And yes, I hope to be back regularly :)