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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Doughboys
November 30, 2020 02:43PM
Hello pt,

The results of the QC has been sent.

Here is the command: 

@animal_warper -input dset_anat_deob -base studytemplatebrain -atlas Brain_label.nii \
-outdir ouput_dir_a_id -ok_to_exist -align_centers_meth OFF -cost nmi -skullstrip mask_brain.nii.gz


afni_proc.py -subj_id a_id -script ouput_dir_a_id + /proc. + a_id -scr_overwrite -out_dir ouput_dir_a_id + / + a_id + .results \
-blocks despike tshift align tlrc volreg blurmask regress \
-dsets dset_bold_deob_RECEN \
-copy_anat dset_anat_deob_RECEN \ 
-anat_has_skull no \
-tcat_remove_first_trs 5 -blip_reverse_dset dset_bold_deob_RECEN_inv \
-align_opts_aea -epi_strip 3dAutomask -cost nmi -giant_move -check_flip \
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -mask_epi_anat yes \       
-tlrc_base studytemplatebrain \
-tlrc_NL_warp -tlrc_NL_warped_dsets ouput_dir_a_id1 + /anatT1_deob_warp2std_nsu.nii.gz \
ouput_dir_a_id1 + /anatT1_deob_shft_al2std_mat.aff12.1D ouput_dir_a_id1 + /anatT1_deob_shft_WARP.nii.gz \ 
-regress_censor_motion 2 -regress_censor_outliers 0.05 -regress_motion_per_run \
-regress_apply_mot_types demean deriv -blur_size 2 -regress_run_clustsim \
 no -regress_est_blur_errts -html_review_style pythonic -execute \

note that:
the functional and the anat were centered prior to these 2 commands
the other sequences didn't have -blip_reverse_dset
and lpc+zz was also used depending on the result of the co-registration (sometimes it just didn't work with lpc+zz and sometimes didn't work with nmi...)

the templates was:
[akjournals.com]
and I am currently trying:
[www.nature.com]

thank you!
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Subject Author Posted

Quality check with AFNI

Doughboys November 30, 2020 11:38AM

Re: Quality check with AFNI

ptaylor November 30, 2020 01:21PM

Re: Quality check with AFNI

Doughboys November 30, 2020 02:43PM