Hello AFNI experts!
I have a perplexing problem. I have previously run amplitude modulation scripts (very very similar to the one I'll share below) and successfully got output for both the #0_coef as well as the #1_coef amplitude modulator. When I looked at the X.xmat.1D file I similarly correctly saw my standard regressor, then my demeaned AM regressor.
However, I re-ran a very similar script (pasted below) and am now no longer seeing the #1_coef output. I am only seeing the standard regressor (#0_coef). Similarly, when I look at the X.xmat.1D plot, I only see my standard regressors, not any AM regressors. I'm wondering what went wrong here? Thank you so much! I have pasted things I hope are helpful below. I'm happy to email/post any other useful information. THANK YOU!
1) Stimulus timing file example for anticipation_agg.1D. there are three runs (three rows) with my onset*AM:duration this is how I had my timing files set up before as well. They were just broken down into conditions (e.g., anticipation_condition1_agg.1D + anticipation_condition2_agg.1D = the file you see here anticipation_agg.1D)
8.451*6:3.016 30.6*2:3.017 41.167*2:3.017 52.734*2:3.016 65.8*2:3.017 78.367*2:3.017 89.934*2:3.016 100*2:3.017 113.567*2:3.017 125.634*2:3.016 138.2*2:3.017 151.267*6:3.016 162.333*5:3.017 186.983*4:3.017 198.55*6:3.017 208.617*2:3.016 220.683*2:3.017 233.25*6:3.017 243.817*6:3.016 256.883*6:3.017 281.033*6:3.017
8.464*4:3.016 30.597*4:3.017 41.164*6:3.016 52.73*6:3.017 65.797*2:3.017 78.363*4:3.017 89.93*2:3.017 113.58*2:3.017 125.647*2:3.016 138.213*2:3.017 151.28*6:3.017 162.347*6:3.016 173.413*5:3.017 186.98*2:3.016 198.546*5:3.017 208.613*5:3.017 220.68*2:3.016 233.246*2:3.017 243.813*2:3.017 256.88*2:3.016 270.446*2:3.017 281.013*2:3.016
8.473*2:3.017 18.54*2:3.016 30.606*2:3.017 41.173*6:3.017 52.74*2:3.016 65.806*2:3.017 78.373*5:3.016 89.939*6:3.017 100.006*6:3.017 113.573*2:3.016 125.639*6:3.017 138.206*2:3.017 151.273*6:3.016 162.339*6:3.017 173.406*6:3.016 186.972*6:3.017 198.539*6:3.017 208.606*6:3.016 220.672*2:3.017 233.239*2:3.017 243.806*2:3.016 256.872*2:3.017 270.439*2:3.016 281.005*2:3.017
2) Here is some output from stats.s1712.HEAD
type = string-attribute
name = BRICK_LABS
count = 398
'Full_Fstat~Ant#0_Coef~Ant#0_Tstat~Ant_Fstat~FB#0_Coef~FB#0_Tstat~FB_Fstat~Resp#0_Coef~Resp#0_Tstat~Resp_Fstat~Missing#0_Coef~Missing#0_Tstat~Missing_Fstat~Task.V.BL_GLT#0_Coef~Task.V.BL_GLT#0_Tstat~Task.V.BL_GLT_Fstat~Ant.V.BL_GLT#0_Coef~Ant.V.BL_GLT#0_Tstat~Ant.V.BL_GLT_Fstat~FB.V.BL_GLT#0_Coef~FB.V.BL_GLT#0_Tstat~FB.V.BL_GLT_Fstat~Resp.V.BL_GLT#0_Coef~Resp.V.BL_GLT#0_Tstat~Resp.V.BL_GLT_Fstat~
3) Here is my individual level analysis script. I am specifying the [1] when setting up my glt's so I'm unsure why I appear to still be getting either the standard regressor alone or a sum of #0 + #1. Thank you!
afni_proc.py -subj_id $subj \
-dsets $subj_dir/func/sub-${subj}_task-seat_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
$subj_dir/func/sub-${subj}_task-seat_run-2_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
$subj_dir/func/sub-${subj}_task-seat_run-3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
-scr_overwrite \
-script $results/$subj/proc.$subj.$GLM \
-out_dir $subj.results.$GLM \
-blocks blur mask scale regress \
-copy_anat $subj_dir/anat/sub-${subj}_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz \
-blur_size 6 \
-regress_est_blur_errts \
-regress_run_clustsim yes \
-regress_stim_times_offset -0.831 \
-regress_stim_times $stimdurmoddir/anticipation_agg.1D \
$stimdurmoddir/feedback_agg.1D \
$stimdurmoddir/response_agg.1D \
$stimdurmoddir/missing_agg.1D \
-regress_stim_labels Ant \
FB \
Resp \
Missing \
-regress_stim_types 'AM1' \
-regress_basis_multi 'dmBLOCK(0)' \
-regress_make_ideal_sum IDEAL_sum.1D \
-regress_motion_file $topdir/derivatives/afni/confounds/sub-${subj}/sub-${subj}_task-seat_allruns_motion.1D \
-regress_motion_per_run \
-regress_extra_ortvec $topdir/derivatives/afni/confounds/sub-${subj}/sub-${subj}_task-seat_allruns_aCompCor6.1D \
$topdir/derivatives/afni/confounds/sub-${subj}/sub-${subj}_task-seat_allruns_cosine.1D \
$topdir/derivatives/afni/confounds/sub-${subj}/sub-${subj}_task-seat_allruns_fd.1D \
-regress_extra_ortvec_labels aCompcor6 cosine fd \
-regress_opts_3dD \
-allzero_OK \
-GOFORIT 8 \
-num_glt 4 \
-gltsym 'SYM: +Ant[1] +FB[1] +Resp[1]' -glt_label 1 Task.V.BL \
-gltsym 'SYM: +Ant[1]' -glt_label 2 Ant.V.BL \
-gltsym 'SYM: +FB[1]' -glt_label 3 FB.V.BL \
-gltsym 'SYM: +Resp[1]' -glt_label 4 Resp.V.BL \
-cbucket cbucket.stats.$subj \
-jobs 30
cd ..
end
