Always one-sided for t-tests. The old
-negative option was a hack just to expedite testing opposing contrasts within the constraints of the old GLM code and with reduced computational time (since prior to
3.0.0, if it weren’t for the
-negative option, you would need to generate the fixel-fixel connectivity matrix independently each time). The
3.0.0 code allows an arbitrary number of t-tests to be defined in the contrast matrix, one line per test, which in terms of capabilities is a superset of just testing the opposite contrast.
Also, I want to make sure that the p values in these two files in fact are the values of 1-p, right?
Correct. I changed the name of the relevant file from “
fwe_pvalue.mif” to “
fwe_1mpvalue.mif” in the hope of better communicating this, but I agree that it’s far from obvious. I would also note that given the various
mrview toolbars now support upper & lower thresholds and the inversion of colour maps, some of the justification for writing p-value data in this form has eroded…