Hello - I am still pretty new to afni. Currently, I am using the TENT function to model BOLD in a block style task. The stimulus times are stacked according to the order of runs in the first column of each text file. When writing the script and flagging -Local times I get the error below:
++ ** GUESSED ** -stim_times 1 using GLOBAL times
*+ WARNING: '-stim_times 1' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 2 using GLOBAL times
*+ WARNING: '-stim_times 2' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 3 using GLOBAL times
*+ WARNING: '-stim_times 3' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 4 using GLOBAL times
*+ WARNING: '-stim_times 4' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 5 using GLOBAL times
*+ WARNING: '-stim_times 5' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 6 using GLOBAL times
*+ WARNING: '-stim_times 6' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 7 using GLOBAL times
*+ WARNING: '-stim_times 7' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 8 using GLOBAL times
*+ WARNING: '-stim_times 8' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
Stim Files are (in ms) for Run1 and Run2 by Block onset in each run:
7.8
134.0
Here is how I scripted it:
3dDeconvolve -input files_by_run.nii \
-polort A \
-num_stimts 8 \
-CENSORTR 1:0..4 \
-CENSORTR 2:0..4 \
-ortvec ${subject}_MovReg.txt motion \
-ortvec ${subject}_CSFReg.txt csf \
-ortvec ${subject}_WMReg.txt wm \
-ortvec ${subject}_WM_GSR_Reg.txt \
-local_times \
-stim_times 1 ${subject}b1.txt 'TENT(0, 30.96,44)' -stim_label 1 b1 \
-stim_times 2 ${subject}b2.txt 'TENT(0, 30.96,44)' -stim_label 2 b2 \
-stim_times 3 ${subject}b3.txt 'TENT(0, 30.96,44)' -stim_label 3 b3 \
-stim_times 4 ${subject}b4.txt 'TENT(0, 30.96,44)' -stim_label 4 b4 \
-stim_times 5 ${subject}b5.txt 'TENT(0, 30.96,44)' -stim_label 5 b5 \
-stim_times 6 ${subject}b6.txt 'TENT(0, 30.96,44)' -stim_label 6 b6 \
-stim_times 7 ${subject}b7.txt 'TENT(0, 30.96,44)' -stim_label 7 b7 \
-stim_times 8 ${subject}b8.txt 'TENT(0, 30.96,44)' -stim_label 8 b8 \
-iresp 1 b1.nii
-iresp 2 b2.nii
-iresp 3 b3.nii
-iresp 4 b4.nii
-iresp 5 b5.nii
-iresp 6 b6.nii
-iresp 7 b7.nii
-iresp 8 b8.nii
-num_glt 12 \
-gltsym "desired contrasts here" label_for contrast \
-rout \
-tout \
-bucket FIR_model_stats.nii \
-GOFORIT 100 \
-noFDR \
-nocout \
-errts Residuals.nii \
-allzero_OK \
-jobs 10
Is there an issue I can change in the way I have organized the 3dDeconvolve commands so I can force the apropriate flag -local_times since the way I have done it (flagged -local_times before stim inputs) does not seem to work?