Hi,

could you please attach a low res snapshot of what you mean by "neck issue"?

If the non-linear registration has worked well, then indeed the easiest is to mask out the neck using fslmaths -mas. You'll need to mask the GM_mod_merg images to calculate the GM volume, and to mask the GM_mask before running randomise.

The best is probably to simply use the 2mm MNI mask of the brain: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask.nii.gz

Hope this helps,
Gwenaëlle

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Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523
Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
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De : jie yu <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Mercredi 9 janvier 2013 11h17
Objet : [FSL] How to edit GM_mask (VBM)

Hi

I guess I can manually modify GM_mask in the stats directory of VBM analysis.

I tried many many times to improve my brain extraction....but I can not remove some neck tissue

And I got some neck tissue in my GM_mask.

Could you please tell me how to manually remove neck tissue in my GM_mask?
I tried BET..... but it did not work well........

Thanks!!!