Contrasts in SPM (with Outtakes!)

We have come to the end of the preprocessing pipeline, and lurch across the finish line with a discussion of contrasts. Often researchers will calculate the difference in beta estimates between two conditions (in SPM, the beta_000?.img files), and also determine whether the difference is significant or not. At the single-subject level both the magnitude of the beta estimate and the variance of the estimate is calculated for each condition, and then t-tests can be performed on these beta estimates by weighting them. For example, the contrast of [1 -1] for Left vs. Right button presses will subtract the beta estimates for the Right button presses from the Left button presses, similar to a paired t-test. A t-statistic is then calculated at each voxel using the following formula:

Where gamma represents the contrast vector (in this example, [1 -1]) and B-hat represents the beta estimates for each condition. The degrees of freedom for a single-subject analysis is based on the number of time points; although, since nearby timepoints share a high degree of correlation, the actual degrees of freedom is pared down to compensate. With most standard processing streams, the variance associated with a beta estimate is discarded when carried to a higher-level analysis, although programs such as FSL's FLAME and AFNI's 3dMEMA take this variance into account when weighting group-level estimates.

Details about how to perform a simple t-contrast in SPM are shown in the following video. The first twenty seconds or so is an outtake where my microphone fell over; we sure like to have fun around here!