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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Bob Cox
March 23, 2017 02:33PM
If you are aligning to the template MNI152_2009_template.nii.gz (part of AFNI binaries), then you can use the #4 sub-brick of that as a gray matter plus CSF mask. You can align to that template using the @SSwarper script supplied with AFNI, for example.

In general, a gray matter mask can only be useful if reasonably high-order nonlinear registration (e.g., 3dQwarp) is used to align the brain to a template. Otherwise, there is too much inter-subject variability for this idea to be useful.
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Cortical mask

Wan Lee March 22, 2017 02:51PM

Re: Cortical mask

Bob Cox March 23, 2017 02:33PM

Re: Cortical mask

Wan Lee March 24, 2017 04:36PM