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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dowdlelt
June 30, 2018 12:47PM
I am guessing here, but I would imagine that including -anat_has_skull no prevents skull stripping from being performed. You are then performing non-linear normalization to the 2009 MNI template, with no skull. That is definitely going to cause problems for the algorithm trying to match the images, and that is my guess for what went wrong.

I've been very fond for using @SSwarper, the AFNI program that performs skull stripping and normalization all in one go, with some tweaks and optimizations. You can use that on your SurfVol in the SUMA folder, and then import the needed files in AFNI proc. This is very useful as you only have to run non-linear normalization, which is slow, just once - so if you decide to run afni_proc again, and again as you tweak settings your life will be much more pleasant.

I've found this recent AFNI publication extraordinarily useful: link to post.
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Subject Author Posted

Resting State proc.py

JW June 29, 2018 04:23PM

Re: Resting State proc.py

dowdlelt June 29, 2018 07:44PM

Re: Resting State proc.py

JW June 30, 2018 12:12PM

Re: Resting State proc.py

dowdlelt June 30, 2018 12:47PM

Re: Resting State proc.py

JW June 30, 2018 02:37PM