Thanks for answering all my questions!!!
>How much is the motion anyway? It seems surprising/disturbing that
>there is a visible amount.
There appears to be 1-3 voxel difference between adjacent slices (1 vox = ~1 mm). It gets worse
toward the top of the head. The scan is 18 min long with 100 slices, in other words it takes about
11sec per slice. Maybe that's too long. I'm still trying to determine whether this is an isolated
problem (me and another subject both had the same problem) or whether long scans are always
corrupted by motion.
Anyway, I'm trying to do motion correction to try to correct the problem. So I concatenated all the
slices into a time series and I ran mcflirt but it didn't work quite right.
1. Is there any way to restrict the motion correction to two dimensions? Mcflirt doesn't seem to
like anything less than 6dof.
2. I just want to confirm that the motion correction is done between adjacent slices. So if I make
slice 0 the reference volume, then slice 1 will be registered to slice 0, and then slice 2 will be
registered to (the now registered) slice 1. Is this correct?
>For truly "bad trials" I would model them as a separate EV
>and then ignore them in the contrasts as this is the best way to "throw away"
>However, it doesn't sound like your events are truly "bad", just very
>long and hence containing more signal power than the short ones. In this case
>I'd still try the full model without modifications.
The problem is that I expect that the subject's decision only takes 500-1000ms, but if the subject
falls asleep, then the trial can take, say, 30 sec. In other words, the subject has his eyes closed for
29 sec and does not have any processing related to the trial. At t=29 sec, the subject opens his
eyes and takes 1 sec to press a button. I think it would be problematic to model this as a 30sec
I like the idea of modeling them as a separate EV and then ingoring them in the contrasts. I think
there are two options for doing this. One is to model slow and fast trials as independent events as
you mentioned above. The other is to model the 30 sec trial as a 1 sec "fast" trial that starts at
t=29 and ends at t=30s, keeping it part of the "fast" EV, then add a second EV of only these
special "corrected" trials and ignoring those in the contrasts. Does this second method make
thanks a lot,