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  

|
November 21, 2022 08:20PM
Hi Rick,
Attached image of the ve2a block. Looks like alignment failed there, too.

Did not include -giant_move, but align_unifize_epi local is included


Here's the command:
afni_proc.py \
-subj_id $name \
-copy_anat $name.T1+orig \
-anat_has_skull yes \
-dsets $name.apt1+orig $name.apt2+orig $name.apt3+orig $name.apt4+orig \
-blocks tshift align tlrc volreg blur mask scale regress \
-align_opts_aea -cost lpc+ZZ -check_flip -align_unifize_epi local \
-tlrc_base TT_N27+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_epi_anat yes \
-blur_size 3.5 \
-blur_in_automask \
-regress_stim_times \
stim_times/$name.NeutAppDec_local.txt \
stim_times/$name.NeutAppInp_local.txt \
stim_times/$name.NeutAmbDec_local.txt \
stim_times/$name.NeutAmbInp_local.txt \
stim_times/$name.NeutAvoDec_local.txt \
stim_times/$name.NeutAvoInp_local.txt \
stim_times/$name.NeutMisDec_local.txt \
stim_times/$name.NeutMisInp_local.txt \
stim_times/$name.AlcAppDec_local.txt \
stim_times/$name.AlcAppInp_local.txt \
stim_times/$name.AlcAmbDec_local.txt \
stim_times/$name.AlcAmbInp_local.txt \
stim_times/$name.AlcAvoDec_local.txt \
stim_times/$name.AlcAvoInp_local.txt \
stim_times/$name.AlcMisDec_local.txt \
stim_times/$name.AlcMisInp_local.txt \
-regress_stim_labels \
NeutAppDec \
NeutAppInp \
NeutAmbDec \
NeutAmbInp \
NeutAvoDec \
NeutAvoInp \
NeutMisDec \
NeutMisInp \
AlcAppDec \
AlcAppInp \
AlcAmbDec \
AlcAmbInp \
AlcAvoDec \
AlcAvoInp \
AlcMisDec \
AlcMisInp \
-regress_stim_types AM1 \
-regress_basis 'dmBLOCK(1)' \
-regress_opts_3dD \
-allzero_OK \
-GOFORIT 11 \
-regress_local_times \
-regress_motion_per_run \
-regress_censor_extern ../rescue_apt_dummyCensor.1D \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.05 \
-regress_compute_fitts \
-regress_est_blur_epits \
-regress_est_blur_errts \
-radial_correlate_blocks tcat volreg \
-html_review_style pythonic \
Attachments:
open | download - Screen Shot 2022-11-21 at 7.17.02 PM.png (2.16 MB)
Subject Author Posted

Possible to start afniproc.py routine at regress step?

mamlung-KU November 16, 2022 03:18PM

Re: Possible to start afniproc.py routine at regress step?

rick reynolds November 16, 2022 06:28PM

Re: Possible to start afniproc.py routine at regress step?

ptaylor November 16, 2022 10:08PM

Re: Possible to start afniproc.py routine at regress step?

mamlung-KU November 17, 2022 04:54PM

Re: Possible to start afniproc.py routine at regress step?

ptaylor November 17, 2022 06:26PM

Re: Possible to start afniproc.py routine at regress step?

mamlung-KU November 21, 2022 12:13PM

Re: Possible to start afniproc.py routine at regress step? Attachments

mamlung-KU November 21, 2022 03:47PM

Re: Possible to start afniproc.py routine at regress step?

rick reynolds November 21, 2022 05:18PM

Re: Possible to start afniproc.py routine at regress step? Attachments

mamlung-KU November 21, 2022 08:20PM

Re: Possible to start afniproc.py routine at regress step? Attachments

mamlung-KU November 21, 2022 11:28PM

Re: Possible to start afniproc.py routine at regress step?

ptaylor November 27, 2022 08:37AM

Re: Possible to start afniproc.py routine at regress step?

ptaylor November 21, 2022 06:31PM

Re: Possible to start afniproc.py routine at regress step?

mamlung-KU November 21, 2022 08:13PM

Re: Possible to start afniproc.py routine at regress step?

ptaylor November 22, 2022 06:31AM

Re: Possible to start afniproc.py routine at regress step?

rick reynolds November 17, 2022 08:33PM