Dear afni experts,
I'd like to use 3dDeconvolve with a block-design paradigm. Each functional run consists of an active block (3 minutes), short break (20 seconds) and a passive block (3 minutes) lasting for 380 seconds in total. The TR is 2.5 s and there are 3 functional scans each of which with 152 volumes. I have used the following arguments to run the command which works with no errors. However, when I plot run-all_X.xmat.1D, the predicted fit for the active block does not match the stimulus timing in 'stim_active.txt' (see the attachments). Based on the plot, it seems that the active block was on during the whole run i.e. form volume 0 to 151 while the .txt file shows that it ends at 180 seconds. I'm not sure what has gone wrong here and would greatly appreciate hearing your thoughts. Thank you!
3dDeconvolve -input run-all.nii.gz \
-concat '1D: 0 152 304' \
-polort 3 \
-num_stimts 2 \
-stim_times 1 stim-active.txt 'BLOCK(180,1)' -stim_label 1 Active \
-stim_times 2 stim-passive.txt 'BLOCK(180,1)' -stim_label 2 Passive \
-gltsym 'SYM: Active -Passive' -glt_label 1 A-P \
-tout -x1D run-all_X.xmat.1D -xjpeg run-all_X.jpg \
-fitts run-all_fitts -bucket run-all_func \
-jobs 10
