AFNI's format for stimulation times associated with duration use a colon between the time and duration. You can generate these "married" parameters with 1dMarry. afni_proc.py can take married stimulus timing files as input with options for the stim_times_type (see afni_proc.py example 7 for AM1 or AM2 stimulus timing). (3dDeconvolve's help has information on using -stim_times_FSL to use the FSL format, but this will be harder to integrate into afni_proc.py). There are lots of options in the 3dDeconvolve help for this, searching for "duration".
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afni.nimh.nih.gov]
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afni.nimh.nih.gov]
Also see this previous posting:
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afni.nimh.nih.gov]
