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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rick reynolds
July 16, 2021 06:00PM
Hi Alena,

Are you getting the 3dFWHMx values from afni_proc.py? If not, what are you using to compute them?

In general, yes, use a mask when running either 3dFWHMx or 3dClustSim.

For 3dttest++, it may be preferable not to use a mask (or to simply run it twice, once masked and once not). It is helpful to have non-masked results, just to see if there are any strange clusters outside the brain. For example, many tasks lead to motion-based results at the edges of the brain, which blur into the brain and can look like valid results if initially masked. It is important to see and try to resolve that. If one doesn't know it happened, well, ouch.

It is simple to use 3dcalc to create a masked 3dttest++ result after the fact, too.

- rick
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Subject Author Posted

using group mask in 3dttest++ with 3dClustsim

astasenko July 16, 2021 02:33PM

Re: using group mask in 3dttest++ with 3dClustsim

rick reynolds July 16, 2021 06:00PM