No Delay

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1

I am working with a mixed block event related design and I am looking for a way to make my block/sustained predictor a boxcar without delay. The model contains cue predictors so I don’t plan on having a ramp up (delay) for the boxcar. Currently I am using block as my basis function for the sustained predictor. If I am not mistaken block is a convolution of a gamma function and a boxcar function and it has a delay. Is there a way to eliminate the delay (ramp up) and is there a pure boxcar function option? I am thinking EXPR might be an option.

Thanks for your time

2

Hello,

Sorry for being slow on this. Sure, you can use the EXPR(b,c) basis function to have a response last from post-stim time ‘b’ to ‘c’. In this case, maybe the expression should just be 1.

For example, if you had tr-locked events on a 2-second grid that lasted for 10s then consider: ‘EXPR(0,10) 1’.
But note that since it includes times at 0 and 10, it will cover 6 time points, not 5. To have only 5, do not quite include the final 10 s offset: ‘EXPR(0,9.9) 1’.

If the events are not TR-locked, you may have to think about what to do when the stimulus lasts for a fraction of the TR. In such a case, timing_tool.py might offer more flexibility. For example, consider the same scenario (10s events, TR=2), but not TR-locked. If you want to include any time point that has at least 30% stimulus time, and if there are 2 runs with durations 300s, consider something like:

timing_tool.py -timing timing.txt -timing_to_1D STIM.1D     \
                         -tr 2.0 -stim_dur 10 -min_frac 0.3             \
                         -run_len 300 300

Consider examples 6 a,b,c in the output of timing_tool.py -help.

  • rick
3

Thanks for your response and I am sorry for my late reply.

I see what you are saying. The end of the 10th second marks the start of the 6th TR assuming a TR of 2 seconds. My stimuli are TR locked with a TR of 1.1 seconds. I want a box car with a duration of 104.5 seconds (95 TRs) and based on your description instead of going with ‘EXPR(0,104.5)1’ I should go with ‘EXPR(0,104.4)1’. I am assuming the one at the end is giving the box car an amplitude of 1.

Thanks Again

4

Sure, that sounds good.

  • rick