Hi Floris-

When using the -nodata flag, you can supply the onset times using the standard -stim_times format. A recently used setup of my own went something like this:

3dDeconvolve -nodata 290 2 -polort 3 -num_stimts 1 -stim_times 1 condA.txt 'GAM' -x1D X.xmat.1D -xjpeg X.jpg

Those times can be in seconds however you would like to specify them (not just TR markers). It is, however, sometimes confusing because the scanner (at least the scanner I have) doesn't write data during that "silent" portion of time. So if you were to have 3 back to back trials (3 sec silent, 4 sec scan), you would end up with 2 data points per trial and thus 2*3 = 6 data points for 3 trials. In essence, according to the written data, it's as if the silent times never happened.

Let me know if that makes sense!

-Peter



Edited 1 time(s). Last edit at 02/16/2016 12:32PM by Peter Molfese.