Hi Beate,

It might be helpful to see both your make_stim_times.py and
3dDeconvolve commands.

1. What you did sounds okay to me. Note that you can make
one long line of 1200 lines (for 1200 seconds across 2
runs) as input to mask_stim_times.py, and it will output
a timing file for 2 runs.

What TR did you input to make_stim_times.py? Since your
stimuli were listed on a 1.0 second grid, that is the TR
you should have entered, rather that the 2.0 second TR
that your data is on.

Just look at the output files, and make sure the first and
last couple of stimulus times are correct for each run.

2. The 3dDeconvolve information message '-stim_times using TR=2 s'
looks okay. It should always be output and match your TR.

3. Using -stim_times, there does not need to be timing grid at
all. So you don't need to tell 3dDeconvolve that the times
are on a 1s grid. The stimulus times can be anything within
your run, that is one of the benefits of using -stim_times.

For example, a -stim_times file might has this for 2 runs:

23.4 56.7 89.012 89.68 92.555
12.8 13.1 14.5 96.8 113.2

Those times have nothing to do with the TR. Note that some
were only .3 or .67 seconds apart. It doesn't matter.

- rick