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Hi - in our default pipeline dtifit is masked using a brain-extracted image - you can change the brain-extraction to give more liberal masking. Cheers. On 1 Oct 2014, at 15:29, Daniel Cox <[log in to unmask]> wrote: > Hi all, > > I'm trying to run TBSS on a dataset of mine but am running into issues with the first step where the FA images are eroded. It seems like too much tissue is being removed, with obvious problems for the later analyses. I've been trying to see whether there is some way to alter the threshold to lower the amount of erosion, but haven't had any luck. Would anyone have any suggestions for how to approach this? > > Thanks, > > Daniel > > > > > <original_FA.png><eroded_FA.png> --------------------------------------------------------------------------- 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 --------------------------------------------------------------------------- Stop the cultural destruction of Tibet