Felix -
> We perform slice timing using SPM99.
> TR = 3 sec
> TA = 2.2 sec
> The gap (pause) of 0.8 sec is at the beginning of the TR, followed by the
> acquisition of the scans.
> 1. Slice timing performs a phase shift, resulting in each time series having
> the values that would have been obtained had the slice been acquired at the
> beginnning of each TR. Does the fact, that the gap is at the beginning of my
> TR, affect my results?
I think that whether you view the gap as occurring at the beginning or end
of a TR (ie before or after slice acquisition) depends on what you define
as time 0 (in your model). If you define time 0 as the very first slice
acquired, then you can view the gap as occurring at the end of each TR.
So I think slice-timing correction will work okay if you enter the TA and TR
as normal. Remember that the correction does not "synchronise" with the start
of the TR; it synchronises with the reference slice that you specify, which
could be the middle of the TA.
Then again, it is quite early in the morning here, so I may not be thinking
clearly... ;-)
> 2. I select the middle slice (in space and time) as reference slice. For
> fMRI analyses, I have to adjust the default sampled bin. To my
> understanding, SPM divides the TR (not the TA) into time bins. Accordingly,
> the middle slice (in time) will not correspond to the middle time bin. Do I
> nevertheless select the middle time bin?
You are correct that it is the TR that is divided into bins. So if you
imagine for a moment that the gap occurred at the end of the TR, and you had
slice-time corrected to the middle slice acquired, then you would need to
set the reference bin (fMRI_T0) to:
fMRI_T0 = round(fMRI_T * (TA / 2) / TR) ( = 6 in your case)
where fMRI_T is the number of bins (default = 16).
Now in your case, I think you could choose this value too, PROVIDED that
you also specify your event onsets with respect to the first ever slice
acquired (ie 0.8s after your first "scan" started). (If an event occurred
before this time, you can enter a negative onset, at least in SPM2).
Rik
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DR RICHARD HENSON
Institute of Cognitive Neuroscience
& Wellcome Department of Imaging Neuroscience
University College London
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