We would be most grateful for assistance with the following issue. We’d like to take a 3d+time file for a single participant (used as input to 3dDeconvolve and 3dREMLfit; normalized, smoothed, clipped, etc.) and transform the BOLD signal for each voxel’s time course into a binary sequence, where a 1 at each time point indicates that the BOLD signal was above a threshold, and 0 indicates that it was below. In other words, we want to create a parallel 3D+time file with binary time courses instead of continuous ones. The reason that we want to do this is so that we can assess the breadth of activation in an ROI, relative to baseline, rather than the ROI’s average activation intensity.
We’d also like to have the flexibility of setting different thresholds, so that we can assess the implications of using different ones. In general, the threshold would be some level of “significance” above the baseline model, at each time point, for each voxel. So, for example, we could define 1 as a voxel showing a BOLD level at a time point that occurs less than 5% of the time in the upper tail of activations for the baseline condition. Alternatively, we could define 1 as an activation occurring <.1% or <20% of the time in the upper tail for the baseline.
We’ve been exploring AFNI tools for how to do this. We could perhaps use 3dmaskdump to create a file with time courses for all voxels in it, which could then be processed to produce a binary version. I’m not sure then, though, how to get this back into a 3d+time image file.
We can also see that –Rbeta for 3dREMLfit produces a baseline model in the beta bucket, specified as polart coefficients that capture the drift in the baseline over time in a given voxel. We can also see that the mean and SD of each voxel time course appears in Graph panels of the AFNI window, which could also be used for this purpose. Perhaps these sources of information could be easily recruited to create the files we’re after.
What we wonder, though, is whether there is a relatively simple and straightforward way to produce the desired files using existing AFNI programs that has escaped our search (such as using 3dSynthesize, 3dcalc, 3dmaskave, 3dttest++, etc.).
Again, we’d be most grateful for any assistance.
Best regards, Larry Barsalou