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 -------------------------------------------------------------------- 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 -------------------------------------------------------------------- ________________________________ 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!!!