Hi there!
I've been trying to figure out how to use the -stim_times_FSL flags with afni_proc.py but am running into some trouble.

Here's an example afni_proc.py call — I'm including the whole thing, but the key elements correspond to the regress block. I'm passing the -stim_times_FSL flag through the -regress_opts_3dD option. After some initial testing, I discovered that I had to manually specify the number of stimulus times with the -num_stimts flag, which I also include in the -regress_opts_3dD option.

afni_proc.py -subj_id ${subj} \
    -script afni_proc_${subj}_alice.tcsh \
    -out_dir ${subj}_alice.proc_py \
    -dsets ${subj}_alice_MB_AP_run0*.nii \
    -blip_reverse_dset ${subj}_alice_SB_PA+orig. -blip_forward_dset ${subj}_alice_SB_AP_run04.nii \
    -blocks volreg mask scale regress \
    -volreg_align_to third \
    -regress_apply_mot_types basic \
    -regress_est_blur_epits \
    -regress_est_blur_errts \
    -regress_opts_3dD \
        -num_stimts 4 \
        -stim_times_FSL 1 ${directory}/timing/alice/cb${cb}/attend_hi.1D 'dmUBLOCK(1)'\
        -stim_label 1 attend_hi \
        -stim_times_FSL 2 ${directory}/timing/alice/cb${cb}/attend_lo.1D 'dmUBLOCK(1)'\
        -stim_label 2 attend_lo \
        -stim_times_FSL 3 ${directory}/timing/alice/cb${cb}/attend_left.1D 'dmUBLOCK(1)'\
        -stim_label 3 attend_left \
        -stim_times_FSL 4 ${directory}/timing/alice/cb${cb}/attend_right.1D 'dmUBLOCK(1)'\
        -stim_label 4 attend_right \
        -gltsym 'SYM: +attend_hi -attend_lo' \
        -glt_label 1 attend_hiVsLo \
        -gltsym 'SYM: +attend_left -attend_right' \
        -glt_label 2 attend_leftVsRight \
        -gltsym 'SYM: +attend_hi +attend_lo -attend_left -attend_right' \
        -glt_label 3 spectralVsSpatial \
    -execute

The 3dDeconvolve command that is generated by this command isn't quite what I want — specifically, there's an extraneous -num_stimts 0 line that gets added in, as well as an -x1D_stop option.

3dDeconvolve -input pb03.$subj.r*.scale+orig.HEAD                            \
    -ortvec dfile_rall.1D mot_basic                                          \
    -polort 3                                                                \
    -num_stimts 0                                                            \
    -num_stimts 4                                                            \
    -stim_times_FSL 1                                                        \
    /Volumes/BlackPanther/alice-in-fmriland/timing/alice/cb1/attend_hi.1D    \
    'dmUBLOCK(1)'                                                            \
    -stim_label 1 attend_hi                                                  \
    -stim_times_FSL 2                                                        \
    /Volumes/BlackPanther/alice-in-fmriland/timing/alice/cb1/attend_lo.1D    \
    'dmUBLOCK(1)'                                                            \
    -stim_label 2 attend_lo                                                  \
    -stim_times_FSL 3                                                        \
    /Volumes/BlackPanther/alice-in-fmriland/timing/alice/cb1/attend_left.1D  \
    'dmUBLOCK(1)'                                                            \
    -stim_label 3 attend_left                                                \
    -stim_times_FSL 4                                                        \
    /Volumes/BlackPanther/alice-in-fmriland/timing/alice/cb1/attend_right.1D \
    'dmUBLOCK(1)'                                                            \
    -stim_label 4 attend_right                                               \
    -gltsym 'SYM: +attend_hi -attend_lo'                                     \
    -glt_label 1 attend_hiVsLo                                               \
    -gltsym 'SYM: +attend_left -attend_right'                                \
    -glt_label 2 attend_leftVsRight                                          \
    -gltsym 'SYM: +attend_hi +attend_lo -attend_left -attend_right'          \
    -glt_label 3 spectralVsSpatial                                           \
    -fout -tout -x1D X.xmat.1D -xjpeg X.jpg                                  \
    -fitts fitts.$subj                                                       \
    -errts errts.${subj}                                                     \
    -x1D_stop                                                                \
    -bucket stats.$subj

I think that because there aren't any stimulus timing files specified outside of the -regress_opts_3dD flag, afni_proc.py is assuming that I don't have any stimulus timing files and automatically adding the -num_stimts 0 flag. Based on the (correct) design matrix that gets generated, it seems that the -num_stimts 4 flag is overwriting this.

The bigger problem is that because the -x1D_stop option is invoked, 3dDeconvolve exits out.

I could manually edit the AFNI commands that are generated by afni_proc.py to remove the two problematic lines (-num_stimts 0 and -x1D_stop) — and indeed, if I do, the 3dDeconvolve command runs perfectly. But I'm wondering if there is something I can add to my afni_proc.py command so that the 3dDeconvolve command gets generated properly.

Thanks!

--
Sahil Luthra, Ph.D. (he/him/his)
Postdoctoral Researcher, Carnegie Mellon University
email: sahil.bamba.luthra@gmail.com
website: sahilluthra.net