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  

|
February 17, 2023 02:04PM
Hello,

I'm new to AFNI and want to run the preprocessing afni_proc.py.
I cannot figure out why it has problems with volreg.

The error message is below:

++ applying anaticor without label, using 3dSeg mask
-- applying input view as +tlrc
-- will use min outlier volume as motion base
** already in tlrc space: -volreg_tlrc_* is not allowed
** invalid block : volreg
----------------------------------------------------------------------
** failed command (create_blocks):

afni_proc.py -subj_id 1002002 -out_dir \
/group/.../1002002_processed -script \
/home/.../scriptss/1002002/1002002 -scr_overwrite -dsets \
/group/.../1002002_V001_DMSRun1.nii -blocks \
despike tshift align tlrc volreg mask blur regress -copy_anat \
/group/northoff/share/sswarper_ang/1002002/anatSS.1002002.nii \
-anat_has_skull no -align_opts_aea -cost lpc+ZZ -big_move \
-volreg_align_e2a -volreg_align_to MIN_OUTLIER -volreg_tlrc_warp \
-tlrc_base MNI152_2009_template_SSW.nii.gz -tlrc_NL_warp \
-tlrc_NL_warped_dsets \
/group/northoff/share/sswarper_ang/1002002/anatQQ.1002002.nii \
/group/northoff/share/sswarper_ang/1002002/anatQQ.1002002.aff12.1D \
/group/northoff/share/sswarper_ang/1002002/anatQQ.1002002_WARP.nii \
-volreg_post_vr_allin yes -volreg_pvra_base_index MIN_OUTLIER \
-mask_segment_anat yes -mask_segment_erode yes -regress_anaticor \
-regress_ROI WMe CSFe -regress_apply_mot_types demean deriv \
-regress_motion_per_run -regress_censor_motion 0.25 \
-regress_censor_outliers 0.1 -blur_size 6.0 -regress_est_blur_epits \
-regress_est_blur_errts -html_review_style pythonic -execute


Thank you very much,
Angelika
Subject Author Posted

** already in tlrc space: -volreg_tlrc_* is not allowed

angelika February 17, 2023 02:04PM

Re: ** already in tlrc space: -volreg_tlrc_* is not allowed

ptaylor February 17, 2023 02:40PM

Re: ** already in tlrc space: -volreg_tlrc_* is not allowed

rick reynolds February 17, 2023 02:48PM

Re: ** already in tlrc space: -volreg_tlrc_* is not allowed

angelika February 23, 2023 02:06PM

Re: ** already in tlrc space: -volreg_tlrc_* is not allowed

rick reynolds February 23, 2023 02:46PM

Re: ** already in tlrc space: -volreg_tlrc_* is not allowed

angelika February 23, 2023 05:14PM

Re: ** already in tlrc space: -volreg_tlrc_* is not allowed

rick reynolds February 23, 2023 05:54PM

Re: ** already in tlrc space: -volreg_tlrc_* is not allowed

angelika February 24, 2023 09:45AM

Re: ** already in tlrc space: -volreg_tlrc_* is not allowed

rick reynolds February 24, 2023 09:59AM