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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Pawel
June 17, 2021 03:11PM
Hi Clem,

sorry for jumping into your thread, but I am a fellow AFNI/NHP/MION user who has been struggling with similar issues.

So you did you get it to work with 3dSkullStrip and -skullstrip_opts -monkey and cost lpa+ZZ, correct?

For me, both 3dSkullstrip and 3dAutomask always failed on a subset of session (each in its own distinct way), but I found out that no epi skullstripping and lpa (without +ZZ) worked surprisingly well for me.

But I never learned about -skullstrip_opts -monkey before, so thank you for this thread, it was educational for me and I am going to test this option on my dataset.
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-epi_strip in afni_proc.py for monkeys

Doughboys June 14, 2021 08:59PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 16, 2021 03:53PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 16, 2021 05:51PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 01:39PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 17, 2021 02:21PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 03:02PM

Re: -epi_strip in afni_proc.py for monkeys

Pawel June 17, 2021 03:11PM

Re: -epi_strip in afni_proc.py for monkeys

Doughboys June 17, 2021 03:32PM

Re: -epi_strip in afni_proc.py for monkeys

ptaylor June 18, 2021 10:29AM