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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June 15, 2016 06:03PM
Thanks! How would I implement this with afni_proc.py?

This is my current call:

afni_proc.py -subj_id ${subj}\
-check_results_dir no\
-script proc_${subj}_AF_new.sh\
-out_dir ${top_dir}${subj}/${subj}.${group_id}.preprocessed\
-dsets ${func_dir}raw_run1+orig.HEAD \
-blocks tshift despike align volreg blur mask regress\
-copy_anat ${struct_dir}struct_ns+orig.HEAD\
-anat_has_skull no\
-tcat_remove_first_trs 0\
-tshift_opts_ts -tpattern alt+z\
-align_opts_aea -giant_move\
-volreg_align_e2a\
-volreg_align_to MIN_OUTLIER\
-blur_size 4\
-mask_apply anat\
-regress_anaticor\
-regress_stim_times\
${stim_times_dir}happy.1D\
${stim_times_dir}angry.1D\
${stim_times_dir}sad.1D\
${stim_times_dir}neutral.1D\
-regress_stim_labels HA AN SA NE \
-regress_basis 'SPMG1'\
-regress_reml_exec\
-regress_est_blur_epits\
-regress_est_blur_errts\
-regress_censor_outliers 0.1\
-regress_censor_motion 0.3\
-regress_apply_mot_types demean deriv\
-regress_opts_3dD\
-GOFORIT 3\
-allzero_OK\
-num_glt 5\
-gltsym 'SYM: +HA[1..4]' -glt_label 1 'HAPPY'\
-gltsym 'SYM: +AN[1..4]' -glt_label 2 'ANGRY'\
-gltsym 'SYM: +SA[1..4]' -glt_label 3 'SAD'\
-gltsym 'SYM: +NE[1..4]' -glt_label 4 'NEUTRAL'\
-gltsym 'SYM: +HA[1..4] +AN[1..4] +SA[1..4] +NE[1..4]' -glt_label 5 'AllBL'\
-jobs 8\

I wasn't able to find documentation on where the "stim_times_AM1" and "dmblock" should fit in.
Subject Author Posted

variable event durations in 3dDeconvolve

mmontchal July 10, 2015 01:21PM

Re: variable event durations in 3dDeconvolve

gang July 10, 2015 05:50PM

Re: variable event durations in 3dDeconvolve

mmontchal June 13, 2016 03:39PM

Re: variable event durations in 3dDeconvolve

rick reynolds June 15, 2016 09:06AM

Re: variable event durations in 3dDeconvolve

mmontchal June 15, 2016 06:03PM

Re: variable event durations in 3dDeconvolve

rick reynolds June 17, 2016 04:05PM

Re: variable event durations in 3dDeconvolve

mmontchal June 17, 2016 05:28PM

Re: variable event durations in 3dDeconvolve

rick reynolds June 17, 2016 08:39PM

Re: variable event durations in 3dDeconvolve

mmontchal June 20, 2016 03:47PM