how to setup stimulus files with local times when one run may be blank

AFNI Message Board
1

Hi

I wanted to ask a question about setting up stimulus files

We are trying to create stimulus files for an experiment with 6 runs. We are using local times with each run on a separate line in the file. The times correspond to user responses - thus there may sometimes be a run with no responses or a blank line in the stimulus file. What is the best way to set this up?

I am pasting all my scripts and one example stimulus file with all 6 runs filled in below

Thank you for much for your help

Sincerely

Prerona

========================================

stimulus file with all 6 runs:

6 27 47 71 95 115 133 152 174 193 215 238 256 275 298 322
6 25 45 69 89 108 130 149 171 193 214 238 262 281 304 324
6 30 48 66 87 109 128 151 173 193 215 237 257 276 296 317
6 28 46 70 90 113 133 153 175 199 219 239 260 283 303 325
6 25 46 68 91 113 131 154 174 197 217 239 259 281 304 328
6 29 51 73 95 114 134 154 176 195 213 237 257 277 297 316

cmd.ap

#!/usr/bin/env tcsh

created by uber_subject.py: version 0.40 (March 30, 2017)

creation date: Mon Oct 2 15:18:13 2017

created by Prerona

set data directories

set top_dir = /nfs/mod/S21101
set stim_dir = /nfs/mod/vectors/

set subject and group identifiers

set subj = S21101
set group_id = subject

run afni_proc.py to create a single subject processing script

afni_proc.py -subj_id $subj
-script proc.$subj -scr_overwrite
-blocks tshift align tlrc volreg blur mask scale regress
-copy_anat $top_dir/S21101.anat+orig
-tcat_remove_first_trs 0
-dsets
$top_dir/S21101.run1.raw+orig.HEAD
$top_dir/S21101.run2.raw+orig.HEAD
$top_dir/S21101.run3.raw+orig.HEAD
$top_dir/S21101.run4.raw+orig.HEAD
$top_dir/S21101.run5.raw+orig.HEAD
$top_dir/S21101.run6.raw+orig.HEAD
-tlrc_base MNI_avg152T1+tlrc
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-volreg_tlrc_warp
-blur_size 4.0
-regress_stim_times
$stim_dir/21101_cue.txt
$stim_dir/21101_error_choice.txt
$stim_dir/21101_error_cog.txt
$stim_dir/21101_feedback.txt
$stim_dir/21101_HL_HP_anticip.txt
$stim_dir/21101_HL_HP_choice.txt
$stim_dir/21101_HL_HP_cog.txt
$stim_dir/21101_HL_LP_anticip.txt
$stim_dir/21101_HL_LP_choice.txt
$stim_dir/21101_HL_LP_cog.txt
$stim_dir/21101_LL_HP_anticip.txt
$stim_dir/21101_LL_HP_choice.txt
$stim_dir/21101_LL_HP_cog.txt
$stim_dir/21101_LL_LP_anticip.txt
$stim_dir/21101_LL_LP_choice.txt
$stim_dir/21101_LL_LP_cog.txt
-regress_stim_labels
cue error_choice error_cog feedback HL_HP_anticip HL_HP_choice
HL_HP_cog HL_LP_anticip HL_LP_choice HL_LP_cog LL_HP_anticip
LL_HP_choice LL_HP_cog LL_LP_anticip LL_LP_choice LL_LP_cog
-test_stim_files yes
-regress_local_times
-regress_basis ‘GAM’
-regress_censor_motion 1.0
-regress_apply_mot_types demean deriv
-regress_opts_3dD
-jobs 3
-regress_compute_fitts
-regress_make_ideal_sum sum_ideal.1D
-regress_est_blur_epits
-regress_est_blur_errts

2

Use an asterisk for those cases where there is no stimulus of a particular type for a specific run. Here’s an excerpt from some old documentation on this:

[size=small]


When using the multi-row input style, you may have the situation where the particular class of stimulus does not 
occur at all in a given imaging run. To encode this, the corresponding row of the timing file should consist of a 
single '*' character; for example, if there are 4 imaging runs but the kth stimulus only occurs in runs 2 and 4, 
then the tname file would look something like this:
  *
  3.2 7.9 18.2 21.3
  *
  8.3 17.5 22.2

[/size]

3

Thank you!