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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
History of AFNI updates
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Hello Paul,
Thank you for your response. Please see my reply in the parent thread - I've updated AFNI to the most current version and it fixed the problem.
Best,
Katya
by
delika
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AFNI Message Board
Hello,
I've updated AFNI from v. 21.0.08 to the most recent v. 21.2.08 and reran @SSwarper with some of the problematic subjects. The alignment was successful in all cases, so it looks like whatever caused the problem was fixed in one of the recent updates!
Best,
Katya
by
delika
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AFNI Message Board
Hello AFNI experts,
I’ve run into a problem with @SSwarper. I use the following command to coregister native T1 images to the MNI template:
@SSwarper \
-base /Users/katya/abin/MNI152_2009_template_SSW.nii.gz \
-input /Vol
by
delika
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AFNI Message Board
Hello Paul,
Thank you for the quick reply! Here's what the output of the @djunct_overlap_check tool looks like for the two problematic subjects (top image - weirdly rotated/stretched brain, bottom image - cut-off parietal lobe).
The tool also produces _DEOB images which show a somewhat closer alignment to the MNI template. I don't do deobliquing as part of my pipeline. Is it somet
by
delika
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AFNI Message Board
Dear AFNI experts,
I would like to ask for your advice on the spatial normalization of anatomical scans.
I warped the individual brains to the MNI template by setting the parameter “ -tlrc_base MNI_avg152T1+tlrc” in afni_proc.py. It worked well for most subjects, but I have a few participants for whom it failed.
The specific problems I have are:
1) The brain images are weirdly rotated
by
delika
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AFNI Message Board