Dear Paul and SPM users,

Just a reminder about TR-depending slice-timing issues.

One thing is to decide until which point slice-timing correction is expected
to improve activation detection (whatever in term of accuracy or sensitivity),
and this point has gotten very useful comments among the recent mails on SPM
list.

However, if someone was interested in comparing EARLY versus LATE Activation
Onset  Times in multi-slice fMRI series, there is virtually no limit for the
TR's values NEEDING a slice-timing correction approach.
I have been using SPM (a couple of years ago, before slice-timing correction
was included in it) contrasting early/late activation's with/without
slice-timing correction (the later was performed elsewhere using Fourier
Interpolation to preserve statistic moments). As expected, in a non corrected
block experiment with 20 slices every 5s, contrasting early versus late
components was essentially showing the slice acquisition scheme (interleaved
in this case). Then, in an event-related experiment, with 18 slices every 2s,
the result was as spectacular than with the block experiment, showing again
very clearly the slice acquisition scheme (also interleaved), even with only
0.111s between each slice.
A straightforward Fourier Interpolation was able to correct quite well those
slice-timing related early/late apparent activation's onset times despite
aliasing of high frequency components. Otherwise, there were only little
changes in term of "activation detection" with/without correction, provided
the response model included a basis of functions covering a sufficient range
of time, something I guess already reported by others in the recent mails.

My feeling is that, if any question related to "early versus late" activation
is to be asked along data analysis, slice-timing correction has certainly to
be the very first post processing step, whatever the used TR. Should it be
reminded that after spatial smoothing (and moreover after normalization), the
slice-related timing errors can be potentially mixed and smoothed enough
through different slices to be completely overlooked when comparing the final
apparent activation onset times?

Pierre-Francois

---------------------------------
Pierre-Francois Van de Moortele, MD, PhD
Center for Magnetic Resonance Research
University of Minnesota
Minneapolis, MN55455
USA
tel: 1-612-626-2001
fax: 1-612-626-2004




> Rik and Richard,
>
> Many thanks for setting me straight re. SOA and TR.
>
> >Thus I would use slice-timing correction for any TR between 0-3s.
>
> My question here really is whether, although the slice timing works best at
> lower TRs, there is some length of TR below which there is no practical
> benefit of using it. In analysing some previous event-related data, I was
> struck by how a relatively sizeable error (about a second) in specifying
> when events occured, there seemed sufficient flexibility in the model to
> cope with the timing problems. That is, when I accidentally modelled all
> events as occuring (approximately) a second later than they actually did,
> the resulting activations (modeled solely with canonical HRF wave) differed
> little from the correctly modelled data. I assumed that this was a result
> of a very blurred temporal reposnse and some degree of flexibility in the
> way that SPM models the responses. This would suggest that the slice timing
> correction, though working best at low TRs, has its least practical value
> at these TRs. Does anyone out there have a feel for whether there is any
> lower limit below which correction for slice timing has lost its value?
>
> (I suppose this may be largely a hypothetical question as, even if there is
> no clear benefit at low TRs, it behoves one to model the data as accurately
> as possible).
>
> Any advice gratefully recieved.
>
> Paul Fletcher
> -----------------------------------------------------------------
> Paul Fletcher,
> Research Department of Psychiatry,
> University of Cambridge,
> Addenbrooke's Hospital,
> Hills Road,
> Cambridge,
> UK
> CB2 2QQ
>
> Tel 01223 336 988
> Fax 01223 336 581