square-wave response model (no convolution) by reading stimtimes from a file?

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1

Hello afni gurus,

Is there a straightforward way to build a square-wave response model (no convolution) by reading stimtimes from a file?

I am modeling a number of tasks with a mixed block-event design. Onset and offset of task blocks vary across tasks and subjects. Currently, I am using -stim_times_AM1 blocktimes.txt with ‘dmBLOCK(1)’ to model the sustained signal, and a set of TENT functions to model the transients associated with block onset and offset. But instead of the ramping inherent to the BLOCK() function, I would like to have the sustained model start instantaneously when the transient model returns to baseline, so that all variance at onset/offset is attributed to transient, and so that there’s no ‘gap’ between sustained and transient.

I’ve fooled around with waver (e.g., waver -EXPR “step(t-4)*step(12-t)” -peak 1 | 1dplot -stdin ), but I have not found a way to build a square wave by using waver while reading stimulus times from a file. It would be great if there were a simple way to do this (or a programmatic way to do something similar on the command line); otherwise it’s not the biggest deal.

Thanks for any thoughts y’all have.

2

Hello,

This post may have gotten lost around Thanksgiving time. Just wondering if you all had any thoughts.

Thanks

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One possibility is to create a regressor that specifies the square-wave (e.g., 1s at the time points of square-wave and 0s for the rest) and then feed it to the option -stim_file in 3dDeconvolve.

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Hello,

Sorry for being slow to reply.

There might be 2 reasonable ways to do this. But to be sure, if the onset is at time t=0 and the duration is 5s, for example, you are hoping to model a square wave from what, 4-12s?

In any case 3dDeconvolve has an ‘EXPR()’ basis function, though it does not incorporate duration modulation.

To make a simple square wave, consider “timing_tool.py -timing_to_1D”. That gives a lot of control, such as the TR, the fraction of the TR that would lead to a ‘1’ in the output, and varying run lengths. Please see examples 6a, b and c from timing_tool.py -help.

  • rick