The user must provide -files, -prefix, -nruns, -nt and -tr, where NT * NRUNS should equal (or be less than) the number of TR lines in each file.
Sample stim_file with 3 stim classes over 7 TRs:
0 0 0 1 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 1
Corresponding stim_times files, assume TR = 2.5 seconds:
stim.01.1D: 2.5 10 stim.02.1D: 5 7.5 stim.03.1D: 15
Options: -files file1.1D file2.1D ... : specify stim files
-prefix PREFIX : output prefix for files
- -run_trs\ TR1 TR2 ... : specify TRs/run, if they differ
- (if same, can use -nruns/-nt)
-nruns NRUNS : number of runs -nt NT : number of TRs per run
-tr TR : TR time, in seconds
-offset OFFSET : add OFFSET to all output times
-labels LAB1 LAB2 ... : provide labels for filenames
-no_consec : do not allow consecutive events
-show_valid_opts : output all options
-verb LEVEL : provide verbose output
complex options:
-amplitudes : “marry” times with amplitudes
This is to make files for -stim_times_AM1 or -stim_times_AM2 in 3dDeconvolve (for 2-parameter amplitude modulation).
With this option, the output files do not just contain times, they contain values in the format ‘time*amplitude’, where the amplitude is the non-zero value in the input file.
For example, the input might look like:
0 2.4 0 0 -1.2On a TR=2.5 grid, this would (skip zeros as usual and) output:
2.5*2.4 10*-1.2
examples:
Given 3 stimulus classes, A, B and C, each with a single column file spanning 7 runs (with some number of TRs per run), create 3 stim_times files (stimes.01.1D, stimes.02.1D, stimes.02.1D) having the times, in seconds, of the stimuli, one run per row.
- make_stim_times.py -files stimA.1D stimB.1D stimC.1D
-prefix stimes1 -tr 2.5 -nruns 7 -nt 100
Same as 1, but suppose stim_all.1D has all 3 stim types (so 3 columns).
- make_stim_times.py -files stim_all.1D -prefix stimes2 -tr 2.5
-nruns 7 -nt 100
2b. Same, but maybe the run lengths differ.
- make_stim_times.py -files stim_all.1D -prefix stimes2 -tr 2.5
- -run_trs 100 110 90 100 110 90 100
Same as 2, but the stimuli were presented at the middle of the TR, so add 1.25 seconds to each stimulus time.
- make_stim_times.py -files stim_all.1D -prefix stimes3 -tr 2.5
-nruns 7 -nt 100 -offset 1.25
An appropriate conversion of stim_files to stim_times for the example in AFNI_data2 (HowTo #5). The labels will appear in the resulting filenames.
- make_stim_times.py -prefix stim_times -tr 1.0 -nruns 10 -nt 272
-files misc_files/all_stims.1D -labels ToolMovie HumanMovie ToolPoint HumanPoint
Generate files for 2-term amplitude modulation in 3dDeconvolve (i.e. for use with -stim_times_AM2). For any TR that has a non-zero value in the input, the output will have that current time along with the non-zero amplitude value in the format time:value.
Just add -amplitudes to any existing command.
- make_stim_times.py -files stim_weights.1D -prefix stimes5 -tr 2.5
-nruns 7 -nt 100 -amplitudes