History of AFNI updates  

|
June 15, 2021 03:15PM
Hi AFNI,
I am running proc py using a T1 in minimum outlier space (via ANTS) and the following script:
########################################
afni_proc.py -subj_id ${subj}\
-script proccomp_${subj}.sh\
-out_dir ${top_dir}${subj}/${subj}.${group_id}.preprocessed_test_anattominout_newcontrasts_reducecollinearity\
-dsets ${func_dir}Test1+orig.HEAD ${func_dir}Test2+orig.HEAD\
-blocks tshift despike align volreg mask blur scale regress\
-copy_anat ${struct_dir}anattominoutlier+orig.HEAD\
-anat_has_skull no\
-tcat_remove_first_trs 0\
-tshift_opts_ts -tpattern alt+z\
-volreg_align_to MIN_OUTLIER\
-blur_size 2\
-regress_anaticor\
-regress_reml_exec\
-regress_opts_reml\
-GOFORIT 10\
-regress_stim_times\
${stim_times_dir}stimtimes.04.1D\
${stim_times_dir}stimtimes.05.1D\
${stim_times_dir}stimtimes.06.1D\
${stim_times_dir}stimtimes.07.1D\
${stim_times_dir}stimtimes.08.1D\
${stim_times_dir}stimtimes.09.1D\
${stim_times_dir}hi_lowNeglureOld.1D\
${stim_times_dir}hi_lowNeglureNew.1D\
${stim_times_dir}hi_lowNeutlureOld.1D
${stim_times_dir}hi_lowNeutlureNew.1D\
${stim_times_dir}hi_lowPoslureOld.1D\
${stim_times_dir}hi_lowPoslureNew.1D\
${stim_times_dir}stimtimes.28.1D\
-regress_stim_labels NegTargHit NegTargMiss NeutTargHit NeutTargMiss PosTargHit PosTargMiss hi_lowNeglureOld hi_lowNeglureNew hi_lowNeutlureOld hi_lowNeutlureNew hi_lowPoslureOld hi_lowPoslureNew No_Resp\
-regress_basis 'GAM'\
-regress_est_blur_epits\
-regress_est_blur_errts\
-regress_censor_outliers 0.1\
-regress_censor_motion 0.5\
-regress_apply_mot_types demean deriv\
-regress_opts_3dD\
-GOFORIT 20\
-allzero_OK\
-num_glt 6\
-gltsym 'SYM: +NegTargHit[1..3] - NegTargMiss[1..3]' -glt_label 1 'NegTargHit -NegTargMiss'\
-gltsym 'SYM: +NeutTargHit[1..3] - NeutTargMiss[1..3]' -glt_label 2 'NeutTargHit -NeutTargMiss'\
-gltsym 'SYM: +PosTargHit[1..3] - PosTargMiss[1..3]' -glt_label 3 'PosTargHit -PosTargMiss'\
-gltsym 'SYM: hi_lowNeglureNew - hi_lowNeglureOld' -glt_label 4 'NegCR - NegFA'\
-gltsym 'SYM: hi_lowNeutlureNew - hi_lowNeutlureOld' -glt_label 5 'NeutCR - NeutFA'\
-gltsym 'SYM: hi_lowPoslureNew - hi_lowPoslureOld' -glt_label 6 'PosCR - PosFA'\
-jobs 8\
#############################################
(cont) My thought is that by aligning the EPI to the minimum outlier and the T1 is already in mimumum outlier space, then anaticor will function just fine.
However, I am trying to reconcile the messages exported to the terminal after proc.py generates the full script. The messages are the following:
#############################################
++ applying anaticor without label, using 3dSeg mask
-- will use min outlier volume as motion base
-- tcat: reps is now 175
++ updating polort to 3, from run len 437.5 s
-- volreg: using base dset vr_base_min_outlier+orig
-- have 7 ROI dict entries ...
++ creating new stim labels: ['stim01', 'stim02', 'stim03', 'stim04', 'stim05', 'stim06', 'stim07', 'stim08', 'stim09']
** WARNING: ANATICOR output now includes zero volumes at
censor points, matching fast ANATICOR and
non-ANATICOR cases
-- no 3dClustSim (since no blur estimation)
+- consider use of: -html_review_style pythonic
-- using default: will not apply EPI Automask
(see 'MASKING NOTE' from the -help for details)
######################################################
(cont) I am wondering if I have missed something in my script. Is it concerning that I would receive these messages? What are the practical implications of ANATICOR including zero volumes at censor points? Even though I include blur in my script, why does AFNI say 'no 3dClustim (since no blur estimation)'?

What does 'updating polort to 3, from run len 437.5 s' mean?

Thanks so much for the help!
Subject Author Posted

Proc Py Message

grangers June 15, 2021 03:15PM

Re: Proc Py Message

ptaylor June 28, 2021 03:13PM



Sorry, only registered users may post in this forum.

Click here to login