I have data from the same subject collected on two different days. Condition A is on the first day and condition B on the second day. I want to compute the contrast A-B. One way is to register the two sessions together, and then analyze the data as if it were from a single session, computing A-B with a 1 -1 glt. A second way is to analyze each session separately, and then do a
3dttest -paired -set1 <sess1data> -set2 <sess2data>
Are these two methods statistically equivalent? Is one preferable over another? Thanks.