Error in skull stripping

AFNI Message Board
1

Dear,

I am conducting skull stripping with 3dSkullstrip, with warning as below:


Warning 3dSkullStrip:****************
 Surface self intersecting! trying again:
 smoothing of 84, avoid_vent -1

It’s difficult for me to figure out what happens to my data, could you give me some idea?

Best,
Peng

2

Hi, Peng-

Did it not produce any output? Check the files at the bottom of this list in the output directory:


ls -ltr

–pt

3

Dear ptaylor,

It does product the anatomical image after skull stripping and the final output of preprocessing for participant 1, but with several successive warning like this for this participant.

I am just curious of what’s happening to make sure it’s been properly operated.

Best,
Peng

4

That’s a typical output warning, and you don’t have to be concerned about this.

5

Dear,

I am just curious of the details of this warning, why it’s saying surface self intersecting? would you mind show more details about this?
Thanks for your great patience and kindness!

Best,
Peng

6

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