> 1. I would like to use slice timing on an fMRI time-series with a TR of
> 2 seconds and 24 slices
> The aquisition sequence was as follows:
>
> slice: 1 5 9 13 17 21 2 6 10 14 18 22 3 7 11 15 19 23 4 8 12 16 20 24
>
> Which would be the best reference slice? Spatially slice 12 is in the
> middle of the scan, but it is the fourth last of all slices to be
> acquired. In the time domain, slice 22 would be in the middle, but
> spatially it is almost on the very top of the scan.
> How much signal has a slice to contain, to be a good reference slice?
I didn't actually do much on the slice timing routine. My contribution
was just a bit of cosmetic stuff so that it used the new SPM image
writing routines. The answer from Rik Henson (who did much more work
on this than myself) is:
`1. The middle slice in time (slice 22) would be best. It doesn't
matter "how much signal is in the reference slice"!'
This is because the timing is most accurate at time points close
to the reference slice, so you minimize the time difference over
all slices in the volume.
Note also that if you have an a priori hypothesis about a particular
region, and you know which plane it is in, then I guess that you would use
that plane as the reference. Of course, this is a little tricky with your
data, but it should be straightforward for simple ascendingly or descendingly
organised images.
Another question that I will try to anticipate before it arises is:
"should the slice time correction be done before or after
the realignment?"
I think this depends. If you have simple ascending or descending data,
then the time difference between adjascent slices should be relatively
small. In this case, I guess you would do the realignment before the
slice time correction.
If you have interleaved slices, then the slice timing correction should
probably be done before realignment (this assumes that most
of the movement is a gradual drift and the position of one image volume
should be close to the position of its neighbours.
Another thing to consider is the lenght of your epochs. If you have longer
epochs, then the slice timing should be less critical.
> 2. The new realigment procedure includes "adjusting sampling errors".
> When running this option on Windows NT, I receive the following error
> message:
>
> Warning: matrix is close to singular or badly scaled
>
> in: ...spm99b\spm_realign.m(Reslice_image) at line 564
>
> and:...spm99b\spm_realign.m at line 370
>
> If I don't adjust for sampling errors, the coregestering and reslicing
> runs perfectly.
> Do you think we have a bug there?
>
> What happens to the data, if I don't adust for sampling errors?
How many scans do you have in the series? If there are less than 8,
then there will be problems.
The adjustment for sampling errors does not actually make that much
difference to the data. It was retained in the code because it
appeared to increase our t-scores a little. The idea was that it
covaried out periodic (1 voxel period) functions of the movement
in order to model the approximations made by a truncated sinc kernel.
It is heavily regularized, and in fact removes only a tiny amount of
signal.
See also messages at http://www.mailbase.ac.uk/lists/spm/search.html
on "Motion parameters as confounds".
Regards,
-John
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