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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January 16, 2019 09:51AM
From 3dSkullStrip's help description, see step #2:

The fully automated process consists of three steps:
  1- Preprocessing of volume to remove gross spatial image 
  non-uniformity artifacts and reposition the brain in
  a reasonable manner for convenience.
    ** Note that in many cases, using 3dUnifize before **
    ** using 3dSkullStrip will give better results.    **
  2- Expand a spherical surface iteratively until it envelopes
  the brain. This is a modified version of the BET algorithm:
     Fast robust automated brain extraction, 
      by Stephen M. Smith, HBM 2002 v 17:3 pp 143-155
    Modifications include the use of:
     . outer brain surface
     . expansion driven by data inside and outside the surface
     . avoidance of eyes and ventricles
     . a set of operations to avoid the clipping of certain brain
       areas and reduce leakage into the skull in heavily shaded
       data
     . two additional processing stages to ensure convergence and
       reduction of clipped areas.
     . use of 3d edge detection, see Deriche and Monga references
       in 3dedge3 -help.
  3- The creation of various masks and surfaces modeling brain
     and portions of the skull

--pt
Subject Author Posted

Error in skull stripping

Peng Ren January 15, 2019 04:10AM

Re: Error in skull stripping

ptaylor January 15, 2019 08:21AM

Re: Error in skull stripping

Peng Ren January 15, 2019 09:41PM

Re: Error in skull stripping

Daniel Glen January 15, 2019 11:58PM

Re: Error in skull stripping

Peng Ren January 16, 2019 01:28AM

Re: Error in skull stripping

ptaylor January 16, 2019 09:51AM