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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
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
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
| December 04, 2017 11:15AM | |
Registered: 11 years ago Posts: 18 |
Hi AFNI experts,
I want to use 3dLSS after using afni_proc.py. Is there a way to do this directly through afni_proc or how can I edit the 3dDeconvolve generated by afni_proc.py to be able to use 3dLSS afterwards? The following is generated by afni_proc.py. Thank you so much!
3dDeconvolve -input pb04.$subj.r*.scale+orig.HEAD \
-censor censor_${subj}_combined_2.1D \
-polort 3 -float \
-local_times \
-num_stimts 38 \
-stim_times_IM 1 \
stimuli/sub-01_task-turntest_animal-foil-DP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 1 ani_fo_DP_lf_go \
-stim_times_IM 2 \
stimuli/sub-01_task-turntest_animal-foil-DP-left-silver.txt 'BLOCK(1,1)' \
-stim_label 2 ani_fo_DP_lf_sl \
-stim_times_IM 3 \
stimuli/sub-01_task-turntest_animal-foil-DP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 3 ani_fo_DP_rg_go \
-stim_times_IM 4 \
stimuli/sub-01_task-turntest_animal-foil-DP-right-silver.txt 'BLOCK(1,1)' \
-stim_label 4 ani_fo_DP_rg_sl \
-stim_times_IM 5 \
stimuli/sub-01_task-turntest_animal-foil-NDP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 5 ani_fo_NDP_lf_go \
-stim_times_IM 6 \
stimuli/sub-01_task-turntest_animal-foil-NDP-left-silver.txt 'BLOCK(1,1)' \
-stim_label 6 ani_fo_NDP_lf_sl \
-stim_times_IM 7 \
stimuli/sub-01_task-turntest_animal-foil-NDP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 7 ani_fo_NDP_rg_go \
-stim_times_IM 8 \
stimuli/sub-01_task-turntest_animal-foil-NDP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 8 ani_fo_NDP_rg_sl \
-stim_times_IM 9 \
stimuli/sub-01_task-turntest_animal-target-DP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 9 ani_ta_DP_lf_go \
-stim_times_IM 10 \
stimuli/sub-01_task-turntest_animal-target-DP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 10 ani_ta_DP_lf_sl \
-stim_times_IM 11 \
stimuli/sub-01_task-turntest_animal-target-DP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 11 ani_ta_DP_rg_go \
-stim_times_IM 12 \
stimuli/sub-01_task-turntest_animal-target-DP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 12 ani_ta_DP_rg_sl \
-stim_times_IM 13 \
stimuli/sub-01_task-turntest_animal-target-NDP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 13 ani_ta_NDP_lf_go \
-stim_times_IM 14 \
stimuli/sub-01_task-turntest_animal-target-NDP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 14 ani_ta_NDP_lf_sl \
-stim_times_IM 15 \
stimuli/sub-01_task-turntest_animal-target-NDP-right-gold.txt \
'BLOCK(1,1)' \
-stim_label 15 ani_ta_NDP_rg_go \
-stim_times_IM 16 \
stimuli/sub-01_task-turntest_animal-target-NDP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 16 ani_ta_NDP_rg_sl \
-stim_times_IM 17 \
stimuli/sub-01_task-turntest_vehicle-foil-DP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 17 veh_fo_DP_lf_go \
-stim_times_IM 18 \
stimuli/sub-01_task-turntest_vehicle-foil-DP-left-silver.txt 'BLOCK(1,1)' \
-stim_label 18 veh_fo_DP_lf_sl \
-stim_times_IM 19 \
stimuli/sub-01_task-turntest_vehicle-foil-DP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 19 veh_fo_DP_rg_go \
-stim_times_IM 20 \
stimuli/sub-01_task-turntest_vehicle-foil-DP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 20 veh_fo_DP_rg_sl \
-stim_times_IM 21 \
stimuli/sub-01_task-turntest_vehicle-foil-NDP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 21 veh_fo_NDP_lf_go \
-stim_times_IM 22 \
stimuli/sub-01_task-turntest_vehicle-foil-NDP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 22 veh_fo_NDP_lf_sl \
-stim_times_IM 23 \
stimuli/sub-01_task-turntest_vehicle-foil-NDP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 23 veh_fo_NDP_rg_go \
-stim_times_IM 24 \
stimuli/sub-01_task-turntest_vehicle-foil-NDP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 24 veh_fo_NDP_rg_sl \
-stim_times_IM 25 \
stimuli/sub-01_task-turntest_vehicle-target-DP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 25 veh_ta_DP_lf_go \
-stim_times_IM 26 \
stimuli/sub-01_task-turntest_vehicle-target-DP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 26 veh_ta_DP_lf_sl \
-stim_times_IM 27 \
stimuli/sub-01_task-turntest_vehicle-target-DP-right-gold.txt \
'BLOCK(1,1)' \
-stim_label 27 veh_ta_DP_rg_go \
-stim_times_IM 28 \
stimuli/sub-01_task-turntest_vehicle-target-DP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 28 veh_ta_DP_rg_sl \
-stim_times_IM 29 \
stimuli/sub-01_task-turntest_vehicle-target-NDP-left-gold.txt \
'BLOCK(1,1)' \
-stim_label 29 veh_ta_NDP_lf_go \
-stim_times_IM 30 \
stimuli/sub-01_task-turntest_vehicle-target-NDP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 30 veh_ta_NDP_lf_sl \
-stim_times_IM 31 \
stimuli/sub-01_task-turntest_vehicle-target-NDP-right-gold.txt \
'BLOCK(1,1)' \
-stim_label 31 veh_ta_NDP_rg_go \
-stim_times_IM 32 \
stimuli/sub-01_task-turntest_vehicle-target-NDP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 32 veh_ta_NDP_rg_sl \
-stim_file 33 motion_demean.1D'[0]' -stim_base 33 -stim_label 33 roll \
-stim_file 34 motion_demean.1D'[1]' -stim_base 34 -stim_label 34 pitch \
-stim_file 35 motion_demean.1D'[2]' -stim_base 35 -stim_label 35 yaw \
-stim_file 36 motion_demean.1D'[3]' -stim_base 36 -stim_label 36 dS \
-stim_file 37 motion_demean.1D'[4]' -stim_base 37 -stim_label 37 dL \
-stim_file 38 motion_demean.1D'[5]' -stim_base 38 -stim_label 38 dP \
-fout \
-tout \
-x1D X.xmat.1D \
-xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.sub-01_task-turntest \
-cbucket sub-01_task-turntest_beta \
-bucket sub-01_task-turntest_stats \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subj \
-errts errts.${subj} \
-cbucket all_betas.$subj \
-bucket stats.$subj
I want to use 3dLSS after using afni_proc.py. Is there a way to do this directly through afni_proc or how can I edit the 3dDeconvolve generated by afni_proc.py to be able to use 3dLSS afterwards? The following is generated by afni_proc.py. Thank you so much!
3dDeconvolve -input pb04.$subj.r*.scale+orig.HEAD \
-censor censor_${subj}_combined_2.1D \
-polort 3 -float \
-local_times \
-num_stimts 38 \
-stim_times_IM 1 \
stimuli/sub-01_task-turntest_animal-foil-DP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 1 ani_fo_DP_lf_go \
-stim_times_IM 2 \
stimuli/sub-01_task-turntest_animal-foil-DP-left-silver.txt 'BLOCK(1,1)' \
-stim_label 2 ani_fo_DP_lf_sl \
-stim_times_IM 3 \
stimuli/sub-01_task-turntest_animal-foil-DP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 3 ani_fo_DP_rg_go \
-stim_times_IM 4 \
stimuli/sub-01_task-turntest_animal-foil-DP-right-silver.txt 'BLOCK(1,1)' \
-stim_label 4 ani_fo_DP_rg_sl \
-stim_times_IM 5 \
stimuli/sub-01_task-turntest_animal-foil-NDP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 5 ani_fo_NDP_lf_go \
-stim_times_IM 6 \
stimuli/sub-01_task-turntest_animal-foil-NDP-left-silver.txt 'BLOCK(1,1)' \
-stim_label 6 ani_fo_NDP_lf_sl \
-stim_times_IM 7 \
stimuli/sub-01_task-turntest_animal-foil-NDP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 7 ani_fo_NDP_rg_go \
-stim_times_IM 8 \
stimuli/sub-01_task-turntest_animal-foil-NDP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 8 ani_fo_NDP_rg_sl \
-stim_times_IM 9 \
stimuli/sub-01_task-turntest_animal-target-DP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 9 ani_ta_DP_lf_go \
-stim_times_IM 10 \
stimuli/sub-01_task-turntest_animal-target-DP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 10 ani_ta_DP_lf_sl \
-stim_times_IM 11 \
stimuli/sub-01_task-turntest_animal-target-DP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 11 ani_ta_DP_rg_go \
-stim_times_IM 12 \
stimuli/sub-01_task-turntest_animal-target-DP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 12 ani_ta_DP_rg_sl \
-stim_times_IM 13 \
stimuli/sub-01_task-turntest_animal-target-NDP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 13 ani_ta_NDP_lf_go \
-stim_times_IM 14 \
stimuli/sub-01_task-turntest_animal-target-NDP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 14 ani_ta_NDP_lf_sl \
-stim_times_IM 15 \
stimuli/sub-01_task-turntest_animal-target-NDP-right-gold.txt \
'BLOCK(1,1)' \
-stim_label 15 ani_ta_NDP_rg_go \
-stim_times_IM 16 \
stimuli/sub-01_task-turntest_animal-target-NDP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 16 ani_ta_NDP_rg_sl \
-stim_times_IM 17 \
stimuli/sub-01_task-turntest_vehicle-foil-DP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 17 veh_fo_DP_lf_go \
-stim_times_IM 18 \
stimuli/sub-01_task-turntest_vehicle-foil-DP-left-silver.txt 'BLOCK(1,1)' \
-stim_label 18 veh_fo_DP_lf_sl \
-stim_times_IM 19 \
stimuli/sub-01_task-turntest_vehicle-foil-DP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 19 veh_fo_DP_rg_go \
-stim_times_IM 20 \
stimuli/sub-01_task-turntest_vehicle-foil-DP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 20 veh_fo_DP_rg_sl \
-stim_times_IM 21 \
stimuli/sub-01_task-turntest_vehicle-foil-NDP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 21 veh_fo_NDP_lf_go \
-stim_times_IM 22 \
stimuli/sub-01_task-turntest_vehicle-foil-NDP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 22 veh_fo_NDP_lf_sl \
-stim_times_IM 23 \
stimuli/sub-01_task-turntest_vehicle-foil-NDP-right-gold.txt 'BLOCK(1,1)' \
-stim_label 23 veh_fo_NDP_rg_go \
-stim_times_IM 24 \
stimuli/sub-01_task-turntest_vehicle-foil-NDP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 24 veh_fo_NDP_rg_sl \
-stim_times_IM 25 \
stimuli/sub-01_task-turntest_vehicle-target-DP-left-gold.txt 'BLOCK(1,1)' \
-stim_label 25 veh_ta_DP_lf_go \
-stim_times_IM 26 \
stimuli/sub-01_task-turntest_vehicle-target-DP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 26 veh_ta_DP_lf_sl \
-stim_times_IM 27 \
stimuli/sub-01_task-turntest_vehicle-target-DP-right-gold.txt \
'BLOCK(1,1)' \
-stim_label 27 veh_ta_DP_rg_go \
-stim_times_IM 28 \
stimuli/sub-01_task-turntest_vehicle-target-DP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 28 veh_ta_DP_rg_sl \
-stim_times_IM 29 \
stimuli/sub-01_task-turntest_vehicle-target-NDP-left-gold.txt \
'BLOCK(1,1)' \
-stim_label 29 veh_ta_NDP_lf_go \
-stim_times_IM 30 \
stimuli/sub-01_task-turntest_vehicle-target-NDP-left-silver.txt \
'BLOCK(1,1)' \
-stim_label 30 veh_ta_NDP_lf_sl \
-stim_times_IM 31 \
stimuli/sub-01_task-turntest_vehicle-target-NDP-right-gold.txt \
'BLOCK(1,1)' \
-stim_label 31 veh_ta_NDP_rg_go \
-stim_times_IM 32 \
stimuli/sub-01_task-turntest_vehicle-target-NDP-right-silver.txt \
'BLOCK(1,1)' \
-stim_label 32 veh_ta_NDP_rg_sl \
-stim_file 33 motion_demean.1D'[0]' -stim_base 33 -stim_label 33 roll \
-stim_file 34 motion_demean.1D'[1]' -stim_base 34 -stim_label 34 pitch \
-stim_file 35 motion_demean.1D'[2]' -stim_base 35 -stim_label 35 yaw \
-stim_file 36 motion_demean.1D'[3]' -stim_base 36 -stim_label 36 dS \
-stim_file 37 motion_demean.1D'[4]' -stim_base 37 -stim_label 37 dL \
-stim_file 38 motion_demean.1D'[5]' -stim_base 38 -stim_label 38 dP \
-fout \
-tout \
-x1D X.xmat.1D \
-xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.sub-01_task-turntest \
-cbucket sub-01_task-turntest_beta \
-bucket sub-01_task-turntest_stats \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subj \
-errts errts.${subj} \
-cbucket all_betas.$subj \
-bucket stats.$subj
| Subject | Author | Posted |
|---|---|---|
|
zhenganglu | December 04, 2017 11:15AM |
