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Hi Markus In FSL4.1.2, the behaviour of the termination mask was such that a tract stopped as soon as it _exited_ a termination mask (as opposed to _entered_) I am not sure if that can explain the results you are getting in fdt_paths. Also: are you using the option --loopcheck (if you don't use this, it may explain finding samples in the other hemisphere that perhaps loop back towards the waypoint mask). The result in waytotal (the text file in the output directory) should be the same whether you have set your waypoint mask as a termination or not. It counts samples that reach the waypoint mask. If samples reach the termination mask, they have also reached the waypoint mask, so they will be counted as well. Note that the number you get with the command "fslstats fdt_paths -M" has a completely different meaning. This number _will_depend on whether you have set your waypoint as termination. It will be smaller in the case where you have a termination mask, since samples will not be counted in voxels passed the termination mask.. Cheers, Saad. On 20 Nov 2009, at 18:08, Markus Gschwind wrote: > Dear Saad and others! > > We notice a strange behavior in our probtrackx result of FSL 4.1.2. > We used a seed sphere in the corpus callosum and applied another > sphere about 3 cm lateral in the splenium as both a waypoint and a > termination mask. > My understanding is that we only should get those regions where fibers > start form the seed and travel to the termination/waypoint. > The resulting fdt_path however shows areas in both hemispheres and > largely behind the termination mask, similar to the use of NO > termination/waypoint. > > I read about the minor bugfix in version 4.1.3. about the termination > mask behavior. > > We would like to know if the waytotal counting actually only contains > the right numbers or if it is including the wrong superfluous paths. > > However the waytotal calculation gives me 33 seedvoxels* 5000 samples > = 165000 for without waypoint > and fslstats fdt_path -M = 2789. 2789 * 33 = 92037 for the use with > waypoint/termination. > > So it seems it somewhat respects the waypoint/termination. But does it > respect both or only the waypoint mask but not the termination? > > As on our server are currently about 4 studies running I would not > update when not absolutely necessary in this particulary case! > > Thanks so much for your help! > Best, Markus > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK +44 (0) 1865 222466 (fax 717) www.fmrib.ox.ac.uk/~saad