Just want to get an opinion on this.
I have been using GAM functions on data from an event related design with stimulus durations of 3 seconds.
First, is 3 seconds too long for use of the GAM function? I know the documentation mentions short presentation times as being between 0-2 seconds. If it is too long, which function might be preferable?
Second, I realize I modeled fixation crosses as one of the trial types in the gltsym. These however are NOT presented for 3 seconds - they are only on screen for about .5-1 seconds between each stimulus presentation. I realize now that this violates the recommendation of having conditions with the same stimulus time. Would you say this might be issue?
If not, great! But if so, would you recommend leaving fixation crosses out of the model to serve as implicit baselines? (That way all modeled trials have the same stimulus length…) Or rather, would it be better to use a different basis function while keeping fixation crosses included in the gltsym?
Sorry for being slow on this…
Yes, 3 seconds is a bit short for a GAM function. You might get a better feel for some of the basis functions using “timing_tool.py -help_basis”, with help for plotting them being shown at the end.
The BLOCK function seems to be a good model, so you can compare how it would model the response to a 3 second event with a GAM function. You can also convolve GAM with a 3 second boxcar. For example, plot GAM, a 3-second GAM, a 1-second BLOCK and a 3-second BLOCK as follows:
3dDeconvolve -nodata 200 0.1 -polort -1 -num_stimts 4 \
-stim_times 1 '1D:0' GAM \
-stim_times 2 '1D:0' 'GAM(8.6,0.547,3)' \
-stim_times 3 '1D:0' 'BLOCK(1,1)' \
-stim_times 4 '1D:0' 'BLOCK(3,1)' \
-x1D X.xmat.1D -x1D_stop
1dplot -one X.xmat.1D
The short functions, GAM (black) and BLOCK(1,1) (green) peak at a similar time, though BLOCK(1,1) is wider. The 3-second GAM (red) peaks about 3 seconds later than GAM, while BLOCK(3,1) (blue) peaks about 2 seconds later than GAM.
We would tend to suggest using the blue BLOCK(3,1). This should help clarify the differences.