Hi Christopher,
You are correct that an HRF would not be appropriate here.
For a sparse event-related analysis, TR = TA (acquisition time). In
your case, this is 4 secs. Instead of the canonical HRF, use a first
order finite impulse response (FIR) function with a window length
corresponding to TA.
If each image volume you acquired = 1 trial, then your onsets for each
experimental condition should reflect this by being a multiple of 4
sec apart with the first trial onset at 0 sec. Alternatively, you
could specify 'units for design' as 'scans' and list the trial onsets
according to their scan number.
There is a little more information in this post:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0703&L=SPM&P=R47367&I=-3
Hope this helps,
Greig
On 15/02/2008, at 12:29 PM, Christopher Benjamin wrote:
> 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
__
Dr Greig de Zubicaray
Senior Research Fellow
fMRI Laboratory, Centre for Magnetic Resonance
University of Queensland, QLD 4072, Australia
Tel: (+617) 3365 4100 (Office)
(+617) 3365 4250 (B106, Ritchie Building)
Fax: (+617) 3365 3833
fMRI Lab Page: http://www.fmrilab.net
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