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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Dmitry
June 07, 2006 09:09AM
Hi! I would like to remove all activation outside the brain. I found the tutorial here: [http://afni.nimh.nih.gov/afni/doc/faq/61/view?searchterm=mask] with an answer to "Q61".

I followed the steps, and the "outside" activation decreases, but some of it still remains, and is especially visible on the axial images. I set AFNI_FIM_BKTHR to 40, as suggested, but that didn't do much. Then I tried increments of 10 up to 99%, but I still get plenty of activation outside of the brain in the axial scans, and some in the sagittal.

Any suggestions as to how I would only leave the in-brain activation? Thanks!
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Subject Author Posted

Masking function outside brain

Dmitry June 07, 2006 09:09AM

Re: Masking function outside brain

Daniel Glen June 07, 2006 09:59AM

Re: Masking function outside brain

Dmitry June 09, 2006 09:35AM

Re: Masking function outside brain

Daniel Glen June 09, 2006 11:34AM