Dear Tommi,
What you describe is a classic "sparse sampling" design in that it meets
all three criteria:
1) the stimuli are presented in silence,
2) the BOLD response to the stimulus is sampled at, or near, its peak in
auditory areas, and
3) you allow sufficient time for the BOLD response to the scanner noise to
return to baseline levels.
Points 2 and 3 distinguish sparse sampling from interleaved or clustered
sampling. If you are interested in auditory cortex responses
uncontaminated by the scanner noise, you need to use sparse sampling. The
important thing about analysing these data is to note that you are not
acquiring BOLD waveforms -- that would require far more frequent
sampling. instead you are acquiring categorical data (like PET data). In
other words, each data point represents a condition being ON or OFF -- it
is not a continuous sampling. So all of the time course issues in fMRI go
out the window. High pass filtering may still be useful but prewhitening
should be turned off (see point 3).
Because you aren't collecting time series data in the true sense, the TR
becomes arbitrary and you certainly don't want to use convolution at
all. Slice timing should also be avoided because it relies on
interpolating temporal responses. Since you didn't collect a waveform, you
can't interpolate on it. For similar reasons, you can't use a temporal
derivative either.
So given these constraints, which were imposed by the data collection
technique used, the TR is meaningless since it is used to handle the fact
that data in typical fMRI experiments are acquired continuously, but each
voxel is acquired discretely. The only function it plays in the sparse
sampling analysis is to specify the event timings. So you might as well
set the TR=1 and then just number your events sequentially using 3-column
format (or use 1-column format if your happy putting all those zeros in).
The many steps which you described in your email would be necessary if you
were using a shorter TR which didn't take point 3 into account (so-called
clustered or inter-leaved acquisition). Then you would be sampling a
continuous waveform in long discrete intervals and you'd have to be very
careful with respect to "jittering" the stimulus onset and the TR
acquisition in order to get an unbiased and sensitive measure. In sparse
sampling, jittering is unnecessary because you presumably did preliminary
testing in order to guarantee that point 2 was met -- namely that the
response in your ROI (auditory cortex in this case) was maximal approx 4-5s
after onset, since that's when you sample the region.
I think Steve is planning to add some of these details to our FAQ soon, if
he hasn't already.
Hope this helps.
Joe
Joseph Devlin, Ph. D.
FMRIB, Dept. of Clinical Neurology
University of Oxford
John Radcliffe Hospital
Headley Way, Headington
Oxford OX3 9DU, U.K.
Phone: +44 (0)1865 222 494
Fax: +44 (0)1865 222 717
Email: [log in to unmask]
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