Hi afni experts,
I have three conditions in my new event-related fMRI experiment: exp1,exp2 & control. I am interested in two t-test pairs among these conditions: exp1-control & exp2-control. So I search the best experiment sequence use the method provided by @stim_analyze: generating sequence using make_random_timing.py, calculating NSD using 3dDeconvolve and choosing the sequence using the criteria with the sum of the NSD of the two t-test pairs.
But the best sequence is very weird. Some events in this sequence are too close in time and some other events' ISI are too long.

The ISI statistics :

data              min      mean     max     stdev
-----------     -------  -------  -------  -------
pre-rest          4.000    9.000   14.000    4.163
post-rest        14.000   28.500   44.000   12.369

run #0 ISI        0.000   12.000   56.000   13.156
run #1 ISI        0.000   13.130   68.000   17.277
run #2 ISI        0.000   12.870   62.000   15.630
run #3 ISI        0.000   12.870   68.000   16.807

all runs ISI      0.000   12.717   68.000   15.542

Visualizing the sequence:

The code used was copied from @stim_analyze without big changes:

set num_stim    = 3
set num_runs    = 4
set pre_rest    = 0
set post_rest   = 6
set min_rest    = 0 
set tr          = 2.0 
set stim_durs   = 2
set stim_reps   = 8 # This specifies the number of repetitions of each stimulus type, per run
@ run_lengths   = $post_rest + $pre_rest + 186 * `printf '%.f' "$tr"` # set the total time, per run (in seconds)
set iterations  = 1000000   # number of iterations to compare
set seed        = 123       # initial random seed
set outdir      = optimal_results
set LCfile      = NSD     # file to store norm. std. dev. sums in
set datapath    = optimal_results
set labels      = "exp1 exp2 control"
# recreate $outdir each time
if ( -d $outdir ) then
   echo "** removing output directory, $outdir ..."
   \rm -fr $outdir
endif
echo "++ creating output directory, $outdir ..."
mkdir $outdir
cd $outdir
echo -n "" > $LCfile
echo -n "iteration (of $iterations): 000000000"
# HRF
#3dDeconvolve -num_stimts 1 -polort -1 -nodata 51 0.5 \
#   -stim_times 1 '1D: 0' 'BLOCK5(1,1)'       \
#   -x1D stdout: | 1dplot -stdin -THICK -del 0.5 -jpeg bk5
# run the test many times
set numlen=`expr length $iterations`
foreach iter (`count -digits $numlen 1 $iterations`)
@ seed = $seed + 1
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 $tr                                                 \
                -tr_locked                                              \
                -max_consec 2                                          \
                -show_timing_stats                                      \
                -save_3dd_cmd cmd.3dd.$iter                             \
                        >& out.mrt.$iter
3dDeconvolve                                                     \
    -nodata 756 2.000                                            \
    -polort 3                                                    \
    -concat '1D: 0 189 378 567'                                  \
    -num_stimts 3                                                \
    -stim_times 1 stimes.${iter}_01_exp1.1D 'BLOCK5(1,1)'    \
    -stim_label 1 Global_constant                                \
    -stim_times 2 stimes.${iter}_02_exp2.1D 'BLOCK5(1,1)'         \
    -stim_label 2 Scr_nature                                     \
    -stim_times 3 stimes.${iter}_03_control.1D 'BLOCK5(1,1)'       \
    -stim_label 3 Scr_constant                                   \
    -jobs 10                                                     \
    -gltsym 'SYM: exp1 -control'                      \
    -glt_label 1 locals                                           \
    -gltsym 'SYM: exp2 -control'                 \
    -glt_label 2 global                                         \
    -x1D X.xmat.1D  >& out.3dD.$iter
set nums = ( `awk -F= '/LC/ {print $2}' out.3dD.$iter` ) 
# make a quick ccalc command
        set sstr = $nums[1]
        foreach num ( $nums[2-] )
            set sstr = "$sstr + $num"
        end
set num_sum = `ccalc -expr "$sstr"`
echo -n "$num_sum = $sstr : " >> $LCfile
echo    "iteration $iter, seed $seed" >> $LCfile
foreach i (`count -digit 1 1 $numlen`)
echo -n '\\b' >>tem.1D 
end
set xxx=`cat tem.1D`
echo -n "${xxx}$iter"
rm -f *.1D cmd.3dd* out.* 
end
echo ""
echo "done, results are in '$outdir', LC sums are in '$LCfile'"
sort -n $LCfile | head -20 > opt_results

I want to know what's wrong with my code.
Thank you in advance!



Edited 4 time(s). Last edit at 05/05/2018 02:38PM by Zhang Yu.