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Hi Saad, I have tried using the waypoint order, but this seems to just diminish the tract volume while keeping the noise. Shall I send you a few zipped files of sample results? Best, Meriel On Thu, Mar 27, 2014 at 11:45 AM, Saad Jbabdi <[log in to unmask]>wrote: > Hi > > The --wayorder option should help you here (or are you already using it, > not clear from your email). > > Other than that, I would need to look at your results to provide more > guidance. > > Cheers > Saad > > > > > > On 27 Mar 2014, at 15:32, Meriel Owen <[log in to unmask]> wrote: > > Hi there, > > I'm trying to use probtrack2 to run tractography from a region in the > brainstem up to the cortex using a seed mask and 3 waypoints (with > exclusion across the midline). Using the default settings, I seem to be > getting inclusion of cingulum and a lot of spurious wisps. I've been trying > to figure out the optimal settings for this analysis but I was hoping you > might be able to suggest some things to help. Is there an optimal > curvature threshold for a path that essentially goes from motor cortex into > the brainstem (almost a straight line)? I tried using the waypoints > specified in their order but this didn't seem to help. I have also tried > using -thrP in fslmaths to threshold, but this still doesn't seem to get > rid of the small random wisps (and ends up cutting into the tract before > those go). This is very high resolution data (1.25mm^3 voxel size) so I'm > hoping to get a crisp result in the end. > > I really appreciate your help! > Best regards, > Meriel > > > -- > 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 > >