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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 18, 2021 08:20PM

Moderator
Registered: 11 years ago
Posts: 2,321

I should also note that instead of calculating nonlinear alignment within afni_proc.py via:

-tlrc_base MNI152_2009_template.nii.gz \

... we typically nowadays recommend running @SSwarper to calculate both the skullstripping (SS) and nonlinear warp to standard space.

The command would be run ahead of time, e.g.:

@SSwarper                                    \
        -input  DSET_ANAT                  \
        -base   MNI152_2009_template_SSW.nii.gz  \
        -subid  ${subj}                          \
        -odir   OUT_DIR

... and then, as noted here in this sliiightly modified clip of the @SSwarper help file, you provide both the skullstripped anatomical (and turning off further skullstripping) and the warp dsets:

|  afni_proc.py                                                  \
  |    [...other stuff here: processing blocks, options...]        \
  |    -copy_anat OUT_DIR/anatSS.${subj}.nii                               \
  |    -anat_has_skull no                                          \
  |   ....
  |    -volreg_tlrc_warp -tlrc_base MNI152_2009_template_SSW.nii.gz              \
  |    -tlrc_NL_warp                                               \
  |    -tlrc_NL_warped_dsets                                       \
  |       OUT_DIR/anatQQ.${subj}.nii                                       \
  |       OUT_DIR/anatQQ.${subj}.aff12.1D                                  \
  |       OUT_DIR/anatQQ.${subj}_WARP.nii

--pt

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Subject	Author	Posted
AFNI_proc.py - A faulty warped brain	Philipp	August 17, 2021 10:14AM
Re: AFNI_proc.py - A faulty warped brain	ptaylor	August 17, 2021 01:48PM
Re: AFNI_proc.py - A faulty warped brain	Philipp	August 18, 2021 05:51AM
Re: AFNI_proc.py - A faulty warped brain	rick reynolds	August 18, 2021 10:39AM
Re: AFNI_proc.py - A faulty warped brain	ptaylor	August 18, 2021 07:59PM
Re: AFNI_proc.py - A faulty warped brain	ptaylor	August 18, 2021 08:20PM
Re: AFNI_proc.py - A faulty warped brain	Philipp	August 19, 2021 08:41AM
Re: AFNI_proc.py - A faulty warped brain	rick reynolds	August 19, 2021 09:05AM
Re: AFNI_proc.py - A faulty warped brain	Philipp	August 20, 2021 11:26AM
Re: AFNI_proc.py - A faulty warped brain	rick reynolds	August 20, 2021 02:58PM
Re: AFNI_proc.py - A faulty warped brain	ptaylor	August 20, 2021 03:19PM
Re: AFNI_proc.py - A faulty warped brain	Philipp	August 21, 2021 03:24AM
Re: AFNI_proc.py - A faulty warped brain	rick reynolds	August 21, 2021 06:59PM