Hi,
I am a little confused here. We collect 2 separate EPIs for 2 separate events (with two visual conditions, vision and no vision). We collect 2 separate EPIs. I was under the impression that if STIM files are correctly defined, both the EPIs can be run in one afni_poc.py. I did a test:
1. Created afni_proc.py with both the runs and stim files with 2 lines (one for each task) and performed BLOCK(30,1) regression and got beta-coefficients for the tasks

2. Created 2 separate afni_proc.py for each task and modified the stim files (one line only). and performed same regression : model: BLOCK(30,1).

Technically, both methods should give same beta coefficients but they don't. Can you please take a look at the proc.py and let me know what is wrong or what is wrong in my understanding.

AFNI proc.py for 2 EPIs:
afni_proc.py -subj_id $sub \
-script $scrpt_file -scr_overwrite -out_dir $out_dir \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat $anat_file \
-tcat_remove_first_trs $TR \
-tshift_opts_ts -tpattern $pattern \
-dsets \
$same_file \
$diff_file \
-align_opts_aea -cost $costopt \
-tlrc_base MNI_avg152T1+tlrc \
-volreg_align_to last \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_to_fwhm \
-blur_size $blur_size \
-blur_in_automask \
-regress_stim_times \
$stim_dir/times_same_vis.1D \
$stim_dir/times_same_nv.1D \
$stim_dir/times_diff_vis.1D \
$stim_dir/times_diff_nv.1D \
-test_stim_files yes \
-regress_stim_labels \
same_vis same_nv diff_vis diff_nv \
-regress_basis_multi \
'BLOCK(30,1)' \
-regress_censor_motion ${motion} \
-regress_opts_3dD \
-tout \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts
-----------------------------------------------------------

For 1 EPI at a time
afni_proc.py -subj_id $sub \
-script $scrpt_file -scr_overwrite -out_dir $out_dir \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat $anat_file \
-tcat_remove_first_trs $TR \
-tshift_opts_ts -tpattern $pattern \
-dsets \
$same_file \
-align_opts_aea -cost $costopt \
-tlrc_base MNI_avg152T1+tlrc \
-volreg_align_to last \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_to_fwhm \
-blur_size $blur_size \
-blur_in_automask \
-regress_stim_times \
$stim_dir/only_same_vis.1D \
$stim_dir/only_same_nv.1D \
-test_stim_files yes \
-regress_stim_labels \
same_vis same_nv \
-regress_basis_multi \
'BLOCK(30,1)' \
-regress_censor_motion ${motion} \
-regress_opts_3dD \
-tout \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts
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