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  

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May 01, 2013 10:13AM
I have had some success copying/modifying an afni_proc.py script to grab the 1) pre-processed files from one "results" directory; 2) the motion estimates (from 3dvolreg); 3) the anatomic; and 4) the stim files. You could then use the modified afni_proc.py script to quickly generate a script doing just the masking (I think this was necessary to get 3dClustSim to run) and regression. Example below, "mystudy" was the first run through, and mystudyTENT is the second run through.

afni_proc.py -subj_id $aSub -script afni_$aSub_mystudyTENT.tcsh -out_dir $aSub.mystudyTENT \
-dsets $aSub.mystudy/*pb03*.HEAD  \
-blocks mask regress \
-copy_files $aSub.mystudy/dfile_rall.1D $aSub.mystudy/*anat_final* \
-regress_stim_times $aSub.mystudy/stimuli/times* \
-regress_stim_labels c1 c2 c3 c4 \
-regress_local_times \
-regress_motion_file $aSub.mystudy/dfile_rall.1D \
-regress_basis 'TENT(-4,14,10)' \
-regress_censor_outliers 0.1 \
-regress_censor_motion 0.3 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_opts_3dD \
-num_glt 11 \
-gltsym 'SYM: +c1[5..8] -c1[0..3]' -glt_label 1 'print' \
... \
-execute
Subject Author Posted

Can I do BLOCK and TENT regression in 1 proc.py?

pshuk May 01, 2013 09:05AM

Re: Can I do BLOCK and TENT regression in 1 proc.py?

rick reynolds May 01, 2013 09:21AM

Re: Can I do BLOCK and TENT regression in 1 proc.py?

pshuk May 01, 2013 09:40AM

Re: Can I do BLOCK and TENT regression in 1 proc.py?

Peter Molfese May 01, 2013 10:13AM

Re: Can I do BLOCK and TENT regression in 1 proc.py?

rick reynolds May 09, 2013 02:28PM