Adrian -
> I would like to ask you a question concerning the procedure that I have been
> following. I applied slice timing to all scans (a combined block and
> event-related design) using these values that were given to me by the local
> MR experts:
>
> Order of slices: [1 3 5 7 9 11 13 15 17 19 21 2 4 6 8 10 12
> 14 16 18 20 22]
> reference slice: 11
> TR: 3
> TA: 3
>
> In subsequent steps, I have always entered the following:
>
> Number of Bins/TR: 15
> Sampled bin: 1
>
> Is this correct or did I make a mistake? Unfortunately, I am still
> struggling to understand the relationship between these parameters.
I am assuming the numbers in your "order of slices" are in Analyze
format - ie 1=bottom slice in space...
If your reference slice is 11 (the 6th slice acquired in time), your
sampled bin should be:
6/22 * 15 ~= 4
Alternatively, if your sampled bin is 1, your reference slice should
be the first slice acquired in time, ie
1
Alternatively, if you would like the reference slice to be the middle
slice acquired in time, you would choose reference slice = 2 (or 21),
and sampled bin = 8 (or 7).
More generally, if o=[1 3 5 7 9 11 13 15 17 19 21 2 4 6 8 10 12 14 16
18 20 22], and the reference slice chosen in slice_timing correction
stage were r, there were n slices, and N sample bins, then the sampled
bin, s:
s=round(find(o==r)*N/n)
(possibly with a minimum of s=1 when n>>N).
I hope these examples make the relationships clear.
> Does this apply to images used for a block design equally?
Yes, though for boxcar regressors, small differences in timing
(eg from a misspecified sampled bin) are likely to have little effect.
Rik
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DR R HENSON
Institute of Cognitive Neuroscience &
Wellcome Department of Cognitive Neurology
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