What does orthogonalizing my contrast mean?
If you’re testing a conjunction, one worry you might have is the the contrasts that make it up don’t have independent distributions – that they are testing, to some degree, the same effect – and thus the calculation of how significant the conjunction of will be biased. If you use SPM to make a conjunction analysis through the contrast manager, it will attempt to avoid this problem by orthogonalizing your contrasts – essentially, rendering them independent of one another. The computation involved is complicated – not just simply checking whether the contrast vectors are linearly independent, although it’s derived from that – but it can be thought of as follows: Starting with the second contrast, check it against the first for independence; if the two are not orthogonal, remove all the effects of the first one from the second, creating a new, fully orthogonal contrast. Then check the third one against the second and the first, the fourth against the first three, and so on. SPM thus succe
