idea:
you could use the gray, white and CSF images produced after segmentation, and combine them into a single mask. When you have those images produced in MNI space (by the SPM 'segment' feature), you can then combine them to create a single binary mask. That mask you can then use to mask out all voxels of your MNI normalized T1 scan that are not in the mask, and you get a skull stripped normalized T1. I use normalized T1s skull stripped that way for papers all the time, works good for me. And you can do it all with the SPM codebase (no mricron) and automize it.
Alternatively, why don't you simply normalize your (mricron related) native space skull stripped images?
Good luck,
Bas
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
Room B.01.1.03
Mail : Huispost B01.206, P.O. Box 85500
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609
Fax : +31 (0)88 7555443
E-mail : [log in to unmask]
Web : http://www.neuromri.nl/people/bas-neggers
: http://www.brainsciencetools.com (CEO)
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________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Chaleece Sandberg [[log in to unmask]]
Sent: Thursday, May 03, 2012 6:47 PM
To: [log in to unmask]
Subject: [SPM] skull-stripping AFTER normalization
Hi all,
I have lesioned brains and I use lesion masking to perform normalization. I would like to be able to use rendered images of the skull-stripped brains for presentation, but when I run the brain extraction tool in MRIcroN, it only works with the original nifti structural files, not the normalized images. Does anyone know why this is so? Does normalization result in an image that's no longer able to be segmented? Is there any way to skull-strip after normalization?
Thanks,
Chaleece
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