First, as you'd guess from the title, the paper mostly describes a MATLAB package for performing RSA. I could easily download the package and start looking at the demos and documentation, but there is a lot in the package, and understanding what all it's capable of (and how exactly it's doing everything) is not a job for an hour or two. It certainly looks worth careful examination, though; I'm particularly interested in the statistical inference functions.
The part I mostly want to comment on is separate from the MATLAB package: the paper suggests using a linear discriminant analysis t-value as a
"We first divide the data into two independent sets. For each pair of stimuli, we then fit a Fisher linear discriminant to one set, project the other set onto that discriminant dimension, and compute the t value reflecting the discriminability between the two stimuli. We call this multivariate separation measure the linear-discriminant t (LD-t) value."This is dense. To unpack it a bit, the idea is that you're using a statistic derived from a classification analysis for the distance metric. They suggest using Fisher linear discriminant analysis (LDA) for the classification algorithm, with two-fold cross-validation, averaging results across the folds. LDA strikes me as a reasonable suggestion, and I assume any sort of reasonable cross-validation scheme (e.g. leave-one-run-out) would be fine.
But, how to derive the a t-value from the cross-validated LDA? The paper's description wasn't detailed enough for me, so I poked around in the toolbox code, and found the fishAtestB_optShrinkageCov_C function in /Engines/fisherDiscrTRDM.m. It looks like they're fitting the discriminant to the training dataset, projecting the test dataset onto the discriminant, then
Anyway, the idea of using a classification-derived distance metric for RSA is appealing, particularly to get a consistent and predictable zero when stimuli are truly unrelated (fMRI examples are often a bit correlated, making correlation-based RSA comparisons sometimes between "not that correlated" and "somewhat correlated", rather than the more interpretable "nothing" and "something").
This RSA matrix (the official term is "RDM") is from a previous post, which I described as "an RSA matrix for a dataset with six examples in each of two classes (w and f)." While the matrix is sensible (w-f cells are oranger - less correlated - than w-w and f-f cells), the matrix should properly be a single value: the distance between w and f.
In other words, to make an RSA matrix (RDM) I needed at least three classes; not multiple examples of two classes. Say the new class is 'n'. Then, my RSA matrix would have w, f, and n along each axis, and we can ask questions like, "is w is more similar to f or n?". That RSA matrix would have just three numbers: the distances between w and f, w and n, and f and n. If using Pearson correlation, we'd calculate those three numbers by averaging (or some other sort of temporal compression, such as fitting a linear model) across the examples of each class (here, w1, w2, w3, w4, w5, w6) to get one example per class, then correlating these vectors (e.g. w with f). If using LDA, we'd (for example) use the first three w and f examples to train the classifier, then test on the last three of each (and the reverse), then calculate the LD-t. (To be clear, you can calculate LD-t with just two classes, it won't really look like an RDM since you just have one value (w-f).)
Nili H, Wingfield C, Walther A, Su L, Marslen-Wilson W, & Kriegeskorte N (2014). A toolbox for representational similarity analysis. PLoS computational biology, 10 (4) PMID: 24743308
UPDATE 17 July 2014: Changed a bit of the text (strikeouts) in response to helpful comments from Hamed Nili. He also pointed out this page, which describes a few other aspects of the paper and toolbox.