Hi Rick,

I like your idea of pretending that the active baseline condition is just another type of stimulus condition.

How would the program know that this extra task is also part of the same condition as the "-post_stim_rest" TRs? Or is there a way to force each run to end with 9 seconds of my baseline 'condition' and set "-post_stim_rest" equal to zero?

Finally, for tests of my plannted GLTs, I am interested in 1) all the conditions together vs baseline and 2) the area under the curve for each of the 8 conditions of interest. Can you help me understand how to specify those to identify their fitness? I am interested in reducing the amount of run time devoted to the baseline condition and want to see if these GLTs will suffer when I start eliminating baseline trials.

Below are my variables and command line.

Best,
Christine

Here are my variables:
set num_stim = 9
set num_runs = 5
set pre_rest = 12 # min rest before first stim (for magnet steady state)
set post_rest = 9 # min rest after last stim (for trailing BOLD response)
set min_rest = 0 # minimum rest after each stimulus
set tr = 0.75 # used in 3dDeconvolve, if not make_random_timing.py
set stim_durs = 15.5 15.5 15.5 15.5 15.5 15.5 15.5 15.5 3
set stim_reps = 4 4 4 4 4 4 4 4 50
set run_lengths = 890
set labels = "label1 label2 label3 label4 label5 label6 label7 label8 baseline"

Here is my [your :)] command line:
make_random_timing.py -num_stim $num_stim -stim_dur $stim_durs \
-num_runs $num_runs -run_time $run_lengths \
-num_reps $stim_reps -prefix stimes.$iter \
-pre_stim_rest $pre_rest -post_stim_rest $post_rest \
-min_rest $min_rest \
-stim_labels $labels \
-seed $seed \
-tr $tr \
-show_timing_stats \
-save_3dd_cmd cmd.3dd.$iter \
>& out.mrt.$iter