AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
July 20, 2022 01:54PM
Srry I should have mentioned in the original post that ANT_WIN_VS_NOWIN and ANT_LOSS_VS_NOLOSS correspond to Win ($1 and $5) vs No Win ($0) and Loss ($1 and $5) vs No Loss ($0), respectively. Each magnitude separated is not listed here. I'd have to include those to the script. In fact, I tried that using the following script, and did not get the same output. Thoughts on how to fix this? Thanks.

# run afni_proc.py to create a single subject processing script
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
Subject Author Posted

afni_proc script help with contrasts

hmolla July 20, 2022 12:40PM

Re: afni_proc script help with contrasts

rick reynolds July 20, 2022 01:02PM

Re: afni_proc script help with contrasts

hmolla July 20, 2022 01:54PM

Re: afni_proc script help with contrasts

ptaylor July 20, 2022 09:39PM

Re: afni_proc script help with contrasts

ptaylor July 20, 2022 09:43PM

Re: afni_proc script help with contrasts

rick reynolds July 21, 2022 09:52PM