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 04, 2008 01:56PM

Hi Srikanth,

Sorry for being slow, many of us were out of town. Please feel
free to "bump" (reply to) your own message in the future, so that
we see it near the top.

You can use 3dSurf2Vol to create an anatomical mask of the cortical
surface from the standard surface maps.

Note that the surface will not accurately follow the contours of any
subject's brain, and so it does not make for a very good gray matter
mask. See example A from "3dSurf2Vol -help", and consider adding a
'-surf_B' option. You might also consider options '-f_p1_mm' and
'-f_pn_mm' to make the surface thicker.

In any case, it is unlikely that you would be satisfied with such a
mask.

- rick

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Subject Author Posted

Gray matter mask

Srikanth Padmala November 25, 2008 10:16PM

Re: Gray matter mask

rick reynolds December 04, 2008 01:56PM