Hi-
I would just like to reformat the afni_proc.py command a bit to help for readability (and ease for adding/editing options). This might help viewing a bit:
afni_proc.py \
-subj_id $subj \
-script proc.$subj \
-scr_overwrite \
-blocks despike tshift align tlrc volreg blur mask \
scale regress \
-copy_anat $anat_dir/anatSS.${subj}.nii \
-anat_has_skull no \
-tcat_remove_first_trs 0 \
-tshift_opts_ts -tpattern seqplus \
-dsets $epi_dir/${subj}.MID.epi+orig. \
-volreg_align_to MIN_OUTLIER \
-tlrc_base $top_dir/nlWarp/MNI152_2009_template_SSW.nii.gz \
-volreg_align_e2a \
-volreg_tlrc_warp \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets $anat_dir/anatQQ.${subj}.nii \
$anat_dir/anatQQ.${subj}.aff12.1D \
$anat_dir/anatQQ.${subj}_WARP.nii \
-blur_size 5.0 \
-mask_epi_anat yes \
-regress_stim_times $stim_dir/loss_0_ant.txt \
$stim_dir/loss_1_ant.txt \
$stim_dir/loss_5_ant.txt \
$stim_dir/loss_ant.txt $stim_dir/win_0_ant.txt \
$stim_dir/win_1_ant.txt \
$stim_dir/win_5_ant.txt $stim_dir/win_ant.txt \
$stim_dir/fix.txt $stim_dir/win_fb_hit.txt \
$stim_dir/win_fb_nhit.txt \
$stim_dir/loss_fb_hit.txt \
$stim_dir/loss_fb_nhit.txt \
-regress_stim_labels L0ANT L1ANT L5ANT LANT W0ANT W1ANT W5ANT WANT \
FIX WFB_HIT WFB_NHIT LFB_HIT LFB_NHIT \
-regress_basis_multi 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' \
'GAM' 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' \
-regress_stim_types times times times times times times times \
times times times times times times \
-regress_censor_motion 0.3 \
-regress_apply_mot_types demean deriv \
-regress_motion_per_run \
-regress_opts_3dD -num_glt 10 \
-gltsym 'SYM: 1.0*WANT -1.0*W0ANT' \
-glt_label 1 ANT_WIN_VS_NOWIN \
-gltsym 'SYM: 1.0*LANT -1.0*L0ANT' \
-glt_label 2 ANT_LOSS_VS_NOLOSS-gltsym \
'SYM: 1.0*WANT -1.0*LANT' \
-glt_label 3 ANT_WIN_VS_LOSS \
-gltsym \
'SYM: 0.5*WANT 0.5*LANT -0.5*W0ANT -0.5*L0ANT' \
-glt_label 4 ANT_W15L15_VS_W0L0 \
-gltsym 'SYM: WFB_HIT -WFB_NHIT' \
-glt_label 5 WINHIT_VS_MISS \
-gltsym 'SYM: LFB_HIT -LFB_NHIT' \
-glt_label 6 LOSSHIT_VS_MISS \
-gltsym 'SYM: 1.0*W1ANT -1.0*W0ANT' \
-glt_label 7 ANT_WIN1_VS_NOWIN \
-gltsym 'SYM: 1.0*W5ANT -1.0*W0ANT' \
-glt_label 8 ANT_WIN5_VS_NOWIN \
-gltsym 'SYM: 1.0*L1ANT -1.0*L0ANT' \
-glt_label 9 ANT_LOSS1_VS_NOLOSS \
-gltsym 'SYM: 1.0*L5ANT -1.0*L0ANT' \
-glt_label 10 ANT_LOSS5_VS_NOLOSS \
-regress_anaticor_fast \
-regress_reml_exec \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no
With that being done, I might suggest:
+ reordering slightly so all sub-options are grouped a bit (for ease of reading)
+ adding some "-align_* ..." options, to help EPI-anatomical alignment and QC
-align_opts_aea -cost lpc+ZZ \
-giant_move \
-check_flip \
+ add in some more options for QC viewing, including TSNR estimation after volreg and the radcor block:
-volreg_compute_tsnr yes \
-radial_correlate_blocks tcat volreg \
+ add in Python QC HTML creation (which is now the default, but I am not sure what version of AFNI you have):
-html_review_style pythonic
... after which, this is the command:
afni_proc.py \
-subj_id $subj \
-script proc.$subj \
-scr_overwrite \
-blocks despike tshift align tlrc volreg blur mask \
scale regress \
-copy_anat $anat_dir/anatSS.${subj}.nii \
-anat_has_skull no \
-dsets $epi_dir/${subj}.MID.epi+orig. \
-tcat_remove_first_trs 0 \
-tshift_opts_ts -tpattern seqplus \
-radial_correlate_blocks tcat volreg \
-align_opts_aea -cost lpc+ZZ \
-giant_move \
-check_flip \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_compute_tsnr yes \
-tlrc_NL_warp \
-tlrc_base $top_dir/nlWarp/MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warped_dsets $anat_dir/anatQQ.${subj}.nii \
$anat_dir/anatQQ.${subj}.aff12.1D \
$anat_dir/anatQQ.${subj}_WARP.nii \
-blur_size 5.0 \
-mask_epi_anat yes \
-regress_stim_times $stim_dir/loss_0_ant.txt \
$stim_dir/loss_1_ant.txt \
$stim_dir/loss_5_ant.txt \
$stim_dir/loss_ant.txt $stim_dir/win_0_ant.txt \
$stim_dir/win_1_ant.txt \
$stim_dir/win_5_ant.txt $stim_dir/win_ant.txt \
$stim_dir/fix.txt $stim_dir/win_fb_hit.txt \
$stim_dir/win_fb_nhit.txt \
$stim_dir/loss_fb_hit.txt \
$stim_dir/loss_fb_nhit.txt \
-regress_stim_labels L0ANT L1ANT L5ANT LANT W0ANT W1ANT W5ANT WANT \
FIX WFB_HIT WFB_NHIT LFB_HIT LFB_NHIT \
-regress_basis_multi 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' \
'GAM' 'GAM' 'GAM' 'GAM' 'GAM' 'GAM' \
-regress_stim_types times times times times times times times \
times times times times times times \
-regress_censor_motion 0.3 \
-regress_apply_mot_types demean deriv \
-regress_motion_per_run \
-regress_opts_3dD -num_glt 10 \
-gltsym 'SYM: 1.0*WANT -1.0*W0ANT' \
-glt_label 1 ANT_WIN_VS_NOWIN \
-gltsym 'SYM: 1.0*LANT -1.0*L0ANT' \
-glt_label 2 ANT_LOSS_VS_NOLOSS-gltsym \
'SYM: 1.0*WANT -1.0*LANT' \
-glt_label 3 ANT_WIN_VS_LOSS \
-gltsym \
'SYM: 0.5*WANT 0.5*LANT -0.5*W0ANT -0.5*L0ANT' \
-glt_label 4 ANT_W15L15_VS_W0L0 \
-gltsym 'SYM: WFB_HIT -WFB_NHIT' \
-glt_label 5 WINHIT_VS_MISS \
-gltsym 'SYM: LFB_HIT -LFB_NHIT' \
-glt_label 6 LOSSHIT_VS_MISS \
-gltsym 'SYM: 1.0*W1ANT -1.0*W0ANT' \
-glt_label 7 ANT_WIN1_VS_NOWIN \
-gltsym 'SYM: 1.0*W5ANT -1.0*W0ANT' \
-glt_label 8 ANT_WIN5_VS_NOWIN \
-gltsym 'SYM: 1.0*L1ANT -1.0*L0ANT' \
-glt_label 9 ANT_LOSS1_VS_NOLOSS \
-gltsym 'SYM: 1.0*L5ANT -1.0*L0ANT' \
-glt_label 10 ANT_LOSS5_VS_NOLOSS \
-regress_anaticor_fast \
-regress_reml_exec \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no \
-html_review_style pythonic
There may be other suggestions for task modeling and things, too.
--pt
