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

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ptaylor
August 05, 2022 10:20PM
Hi, Mingbo-

I will let Rick way in for other/better ideas, but I think that in your code, you would want to adjust more if you don't want to warp to standard space. Namely, you should remove the "tlrc" block from the list of processing blocks, and all "-tlrc..."-named options (in addition to removing "-volreg_tlrc_warp", which you have already done). Therefore, your command would read: 
afni_proc.py -out_dir $subj.results -subj_id $subj \
#-blocks despike tshift align tlrc volreg mask scale regress \
-blocks despike tshift align   volreg mask scale regress \
-script $subj/proc.$subj.test -scr_overwrite \
-radial_correlate_blocks volreg \
-copy_anat $fs_dir/brain.finalsurfs.nii.gz \
-anat_has_skull no \
-anat_follower anat_w_skull anat $fs_dir/${subj}_SurfVol.nii \
-anat_follower_ROI aaseg anat $fs_dir/aparc.a2009s+aseg.nii.gz \
-anat_follower_ROI aeseg epi $fs_dir/aparc.a2009s+aseg.nii.gz \
-anat_follower_ROI aaseggm anat $fs_dir/aparc.a2009s+aseg_REN_gmrois.nii.gz \
-anat_follower_ROI aeseggm epi $fs_dir/aparc.a2009s+aseg_REN_gmrois.nii.gz \
-anat_follower_ROI FSvent epi $fs_dir/aparc.a2009s+aseg_REN_vent.nii.gz \
-anat_follower_ROI FSwmat epi $fs_dir/aparc.a2009s+aseg_REN_wmat.nii.gz \
-anat_follower_erode FSvent FSwmat \
-dsets $str_dsets \
-tshift_opts_ts -tpattern @$all_out_dir/../slice_timing.txt \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
#-tlrc_base MNI152_2009_template_SSW.nii.gz \
#-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_post_vr_allin yes \
-volreg_pvra_base_index MIN_OUTLIER \
-volreg_align_e2a \
-mask_epi_anat yes \
-regress_motion_per_run \
-regress_ROI_PC FSvent 3 \
-regress_ROI_PC FSwmat 3 \
-regress_ROI_PC_per_run FSvent FSwmat \
-regress_make_corr_vols aeseggm FSvent \
-regress_apply_mot_types demean deriv \
-html_review_style pythonic
... where you could remove the lines starting with "#"---I just put them there to demonstrate what I removed.

--pt
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Subject Author Posted

a possible bug in afni_proc.py

Mingbo August 04, 2022 08:44AM

Re: a possible bug in afni_proc.py

ptaylor August 05, 2022 10:20PM

Re: a possible bug in afni_proc.py

rick reynolds August 09, 2022 11:17AM

Re: a possible bug in afni_proc.py

Mingbo August 14, 2022 10:58PM

Re: a possible bug in afni_proc.py

rick reynolds August 15, 2022 11:29AM

Re: a possible bug in afni_proc.py

Mingbo August 16, 2022 04:22PM

Re: a possible bug in afni_proc.py

rick reynolds August 17, 2022 12:48PM