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

History of AFNI updates  

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Daniel Glen
August 02, 2010 10:49AM
We have done some similar alignment and skullstripping. Because rat brains are imaged in many different ways, it's difficult to know ahead of time which methods will work. 3dIntracranial and 3dAutomask may be useful alternatives to 3dSkullStrip. You can use the "-rat_align" option for align_epi_anat.py (which calls 3dAllineate). To compare similar types of images, the lpa or nmi cost functionals work best with the "-cost" option. In some cases, the "-edge" option helps align images that change in intensity.
Subject Author Posted

3dSkullStrip on mouse/rat/rodent

Nachiket Nadkarni June 23, 2008 05:38AM

Re: 3dSkullStrip on mouse/rat/rodent

Uenal Sakoglu July 30, 2010 03:08PM

Re: 3dSkullStrip on mouse/rat/rodent

Daniel Glen August 02, 2010 10:49AM

Re: 3dSkullStrip on mouse/rat/rodent

craigmichaelm September 23, 2014 03:32PM

Re: 3dSkullStrip on mouse/rat/rodent

ziad September 23, 2014 06:02PM