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
December 16, 2022 03:24PM
Hi JW,

Sorry we did not get back to you on this.

It is preferable to make the masks based on the functional data. Alternatively, you could start with the brain mask datasets output by FreeSurfer and interect, fractionally intersect or take the union of them using 3dmask_tool.

What we like to do is create masks from the functional data intersected with those of the anatomical images, just to keep them tight.

Note that masking can be applied after 3dMVM. It is nice to scrutinize group results for oddities or artifacts, and not just see masked results from the beginning. Masking could be applied as you correct for multiple comparisons.

Do the ASL volumes lend themselves to reasonable masking (e.g. with 3dAutomask)?

- rick
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Creating mask for group level analysis

JW December 04, 2022 04:06PM

Re: Creating mask for group level analysis

rick reynolds December 16, 2022 03:24PM