I have three .niis from the same session, two of these contain condition A, and the third contains condition B. I want to produce subject level t/z maps for A > B and B > A. Following the tutorial here, I was able to make design matrices individually for the three runs and can fit the GLM. However, I am now running into troubles defining the contrasts for a few reasons: 1) the design matrices are different sizes between the condition A and B runs since they are different lengths, 2) I don’t see how I can define a contrast vector, since the conditions I am interested in may be the first conditions of the given runs. That is, I can’t think of a way to make one-hot encoded vectors unique to my contrasts, unless I make them 2D which I’m not sure Nilearn would accept.
Does anyone have any advice about how to proceed in this case?