Dear Christopher,
TR is a well defined term from NMR and indicates the time between
subsequent excitations of, in the case of (f)MRI, a certain proton. It
is sometimes misinterpreted by fMRI users as being the duration of a
scan.
For most EPI sequences, including Sparse EPI, TR should equal the time
between scans including the time you do not read nor excite any signal
in your design. Please note that TR can be (much) shorter than scan
duration, for example for 3D EPI it is a few 10s of ms (so TR does not
per se equal scan duration!!!). Beware when choosing your flip angle, it
should incorporate that you have a very long TR.
Only for the settings of your slice timing correction, I think, you
should notice the fact that the acquisition of you slices is terminated
long before a proton feels an RF excitation again. Otherwise, I think
you can enter TR (in model specification) as being the time between
subsequent exciations of a certain slice, eg the time you acquire a
volume plus the 'silent time'. Enter your onsets in seconds, or in scans
(in the latter case, in units of TR including silent time).
I have no experience with sparse designs though, just my 2 cts from a
theoretical point of view.
Good luck,
Bas
--------------------------------------------------
Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
Room B.01.1.03
Mail : Huispost B.01.206, P.O. Box 85500
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609
Fax : +31 (0)88 7555443
E-mail : [log in to unmask]
Web : http://www.fmri.nl/people/bas.html
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-----Oorspronkelijk bericht-----
Van: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
Namens Christopher Benjamin
Verzonden: vrijdag 15 februari 2008 3:30
Aan: [log in to unmask]
Onderwerp: [SPM] Sparse efMRI, TR, Interscan Interval & SOTs
Dear SPMers
I'm still unable to resolve the issue below and am hoping to clarify,
as I cannot see the solution. Specifically, when running an efMRI
paradigm with a large interval between acquisitions, does 'Interscan
Interval' = TR in the level 1 model (as it notes in the manual, and in
the chapter 27 - face data - example), or does it include the silent
period?
If it is the TR, I assume to proceed you adjust your stimulus onset
times relative to each scan. It looks like this is what was done in
the face data example, as, the TR is listed as 2 secs, indicating the
experiment ran for at least 702 seconds (351 images), but the SOTS do
not go past 351 secs.
If so, is it the case that SPM cannot accommodate a design where
stimulus onsets occur more than a TR's length before scan
acquisition? Here, when you make the first SOT 0secs, the second SOT
occurs before the first.
A related query: If 'Interscan Interval' = TR, I am also wondering if
specifying the SOTS relative to the scan onset times and ignoring the
silent period between scans could create problems. Doesn't SPM need
the full time course of the experiment (inc. silent periods) to
correctly convolve the SOTs with the HRF? Without the full time
course wouldn't it treat each stimulus as activating a region from
resting state, and ignore the effects of repeated activation, thus
modeling the activation incorrectly?
Any advice much appreciated.
Christopher Benjamin
> Dear list,
>
> I am relatively new to SPM and have a quick query about model
> specification for a sparse event-
> related fMRI design.
>
> Specifically, in my design I have a TR of 4 seconds and the delay
> between one TR commencing and
> the next is 16.5 seconds (to allow for stimulus presentation and the
> HRF). In level one model
> specification would I
> - specify 16.5 for the Interscan Interval (not the 4s TR);
> - specify the SOTs in one long train (seconds) relative to the first
> SOT (specified as time = 0; Nb.
> have set Units of design = seconds, time bins = number of slices).
>
> Many thanks
>
> Christopher
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