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Hi Most likely scenario is those seeds are not within the brain mask in diffusion space. Cheers Saad On 6 Dec 2013, at 01:45, wen.zhang55 <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear all, Hi, I have problems with probtrack result while doing from seed vertexes to whole brain mask. The output of seeds * mask matrix indicates that several seeds have no connection to any point of brain (rows filled up with zeros). I checked the seed mask, all of them were in the Wm/Gm surface. So I am quite confused about this phenomenon, how does this happen ? Thank you ! best, Cowen 2013-12-06 ________________________________ wen.zhang55 -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>