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Hi - in general small errors in the BET outline should not be a problem - I would run the full registration process and ascertain that the all_FA images look ok, in which case all is well. Cheers. On 26 Jul 2007, at 12:16, Agnieszka Burzynska wrote: > Dear all, > I am preparing my data for tbss and I believe having a good binary > mask is > crucial for good registration and other steps. After using default bet > setting from GUI I see that ofen the ventral part of medial prefrontal > cortex is cut off. If I manipulate with -g and -f from the command > line, I > et it better, but then too much of non-brain voxels are included > (like in > longitudinal fissure or on bottow of the brain). > > Is there any ´gold standard´for bet for dtifit/tbss? > > How the FA maps registration can be affected by too much non-brain > matter? > > Is it recommended to first center my images and use avwroi to cut > the sides > of the image to improve the bet results? Or as long as the mask is > ´roughly > ok´I can be happy with the outcome? > > Thank you, > Aga ------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---