When the segmentation fails, the first thing to check is that the orientation and origin of the image matches the MNI template orientation and origin. You can check this using checkreg. If it doesn't match, then you can use the Display function to reorient the image. If it matches, then another person on the list might have some suggestions. In my experience, all the failures in my data have been due to orientation issue or image quality issues.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Thu, May 7, 2015 at 1:33 AM, Marris Atwood <[log in to unmask]> wrote:

Hi SPM experts,

As a newbie to SPM and VBM, I have been following John's detailed tutorial on how to perform VBM with SPM.

In the segmentation step, I follow John's advice, leaving many settings as default, and it works perfectly fine for most of the time. It fails only once for all my ~1000 subjects.

I have attached the screenshots of the segmented GM, WM, and CSV for that failure case. Could anyone kindly help analyze the reason why the results look like that? It would be wonderful if one could also point me which parameter I should fine tune in order to fix this.

Thank you all very much in advance!
Marris