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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ptaylor
April 11, 2022 10:46AM
Hi, Dong-

Yes, this is a classic case of "identifying brain/nonbrain looks easy to the eye, but the computer doesn't quite get it". Whether this will have deep affects on further analysis, depends on what you are trying to do. And note that 3dAutomask is often meant to be a quick-and-convenient approximation, and not a quantitative brain masking approach. So, what are you aiming to do?

Re. ways of improving/tweaking 3dAutomask: You could use the "-clfrac .." option, such as "-clfrac 0.6". Perhaps "-peels 2" might help. But note that these kinds of refinements can be very scanner-by-scanner and subject-by-subject.

--pt
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Get the brain mask using 3dAutomask Attachments

Dong April 10, 2022 05:41AM

Re: Get the brain mask using 3dAutomask

ptaylor April 11, 2022 10:46AM

Re: Get the brain mask using 3dAutomask

Daniel Glen April 11, 2022 01:13PM

Re: Get the brain mask using 3dAutomask

RWCox April 12, 2022 04:33PM