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

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_durai_
June 10, 2014 01:34PM
Thanks Rick, indeed it was based on example 8. Here is the command used to generate the script:

# afni_proc.py -subj_id 403 -script afni_psk_403.tcsh -out_dir \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/403.proced -blocks \
# tshift align tlrc volreg surf blur mask scale regress -dsets \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/PSK403_EP_run4+orig \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/PSK403_EP_run5+orig \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/PSK403_EP_run6+orig \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/PSK403_EP_run7+orig \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/PSK403_EP_run8+orig \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/PSK403_EP_run9+orig \
# -copy_anat \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/PSK403_MP.ns.nii \
# -surf_anat \
# /home/owner/Desktop/freesurfer/subjects/PSK403/SUMA/PSK403_SurfVol+orig \
# -surf_spec \
# /home/owner/Desktop/freesurfer/subjects/PSK403/SUMA/PSK403_lh.spec \
# /home/owner/Desktop/freesurfer/subjects/PSK403/SUMA/PSK403_rh.spec \
# -anat_has_skull no -tshift_opts_ts -tpattern alt+z2 -tlrc_opts_at \
# -init_xform AUTO_CENTER -align_opts_aea -giant_move -volreg_align_to \
# first -volreg_tlrc_warp -blur_size 6 -regress_stim_times \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/Cue_Time.txt \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/NR_Neg.txt \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/NR_Neu.txt \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/NR_Pos.txt \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/R_Neg.txt \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/R_Neu.txt \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/R_Pos.txt \
# /home/owner/task1/rontask_Data/RON3/data/PSK403/timing/NoResponse.txt \
# -regress_stim_labels Cue NoRew_Neg NoRew_Neu NoRew_Pos Rew_Neg Rew_Neu \
# Rew_Pos NoResponse -regress_local_times -regress_basis \
# 'GAM(8.6,0.547,2)' -regress_est_blur_epits -regress_est_blur_errts \
# -regress_censor_outliers 0.1 -regress_censor_motion 0.3 \
# -regress_opts_3dD -num_glt 16 -xjpeg \
# ./PSK403_shftNSI_MainExp_Shapefixed.png -gltsym 'SYM: NoRew_Neg \
# -NoRew_Neu' -glt_label 1 NoRew_NegVsNoRew_Neu -gltsym 'SYM: Rew_Neu \
# -NoRew_Neu' -glt_label 2 Rew_NeuVsNoRew_Neu -gltsym 'SYM: Rew_Neg \
# -Rew_Neu' -glt_label 3 Rew_NegVsRew_Neu -gltsym 'SYM: Rew_Neg \
# -NoRew_Neg' -glt_label 4 Rew_NegVsNoRew_Neg -gltsym 'SYM: Rew_Pos \
# -NoRew_Pos' -glt_label 5 Rew_PosVsNoRew_Pos -gltsym 'SYM: NoRew_Pos \
# -NoRew_Neu' -glt_label 6 NoRew_PosVsNoRew_Neu -gltsym 'SYM: Rew_Pos \
# -Rew_Neu' -glt_label 7 Rew_PosVsRew_Neu -gltsym 'SYM: Rew_Pos -Rew_Neg' \
# -glt_label 8 Rew_PosVsRew_Neg -gltsym 'SYM: NoRew_Pos -NoRew_Neg' \
# -glt_label 9 NoRew_PosVsNoRew_Neg -gltsym 'SYM: Cue' -glt_label 10 \
# General_Cue -gltsym 'SYM: NoResponse' -glt_label 11 General_NoResponse \
# -gltsym 'SYM: Rew_Neg +Rew_Neu +NoRew_Neg +NoRew_Neu +Rew_Pos \
# +NoRew_Pos' -glt_label 12 General_Out -gltsym 'SYM: Rew_Neg +Rew_Neu \
# +Rew_Pos -NoRew_Neg -NoRew_Neu -NoRew_Pos' -glt_label 13 Main_Rew \
# -gltsym 'SYM: Rew_Neg -Rew_Neu +NoRew_Neg -NoRew_Neu' -glt_label 14 \
# Main_Emo_Neg -gltsym 'SYM: Rew_Pos -Rew_Neu +NoRew_Pos -NoRew_Neu' \
# -glt_label 15 Main_Emo_Pos -gltsym 'SYM: -Rew_Neg +Rew_Neu +NoRew_Neg \
# -NoRew_Neu' -glt_label 16 Interaction -jobs 8 -GOFORIT 20
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Subject Author Posted

Surface Automask error in afni_proc.py

_durai_ June 10, 2014 01:04PM

Re: Surface Automask error in afni_proc.py

_durai_ June 10, 2014 01:06PM

Re: Surface Automask error in afni_proc.py

rick reynolds June 10, 2014 01:10PM

Re: Surface Automask error in afni_proc.py

_durai_ June 10, 2014 01:34PM

Re: Surface Automask error in afni_proc.py

rick reynolds June 10, 2014 01:49PM

Re: Surface Automask error in afni_proc.py

Peter Molfese June 10, 2014 02:08PM

Re: Surface Automask error in afni_proc.py

_durai_ June 10, 2014 02:13PM

Re: Surface Automask error in afni_proc.py

rick reynolds June 10, 2014 02:16PM