Hi Doug,

I need your recommendations on two topics. I really appreciate your help.

1.) I have two runs of the same experiment, each for about 12 minutes.
These 2 runs are different only in the presentation order of the stimuli. I
also have one localizer session which first, I calculated my contrasts in
it, found the active voxels with positive values, and made a mask of those
voxels. Then, mapped the masks on those 2 runs and got the raw data within
those voxels. So far, so good. Now, I am looking at the Beta values in
these 2 runs for those active voxels, they are very different from each
other. For example, in the first run, they are mostly positive but in the
second run, they are mostly negative. My intuition was that they should be
in the same ballpark. I cannot make sense of this. Do you have any
suggestions on why this is happening?

2.) To calculate the % signal change, is it ok to pick the baseline
whatever is suitable to my research question. For example, if I need to
know the % signal change relative to* the average signal in the first TR of
a specific block*, can I use that as a baseline? Or does it always need to
be the rest or the mean?

Thank you so much and looking forward to hearing from you.

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