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Hi Saad, Sorry if I wasn't clear. I want to keep the tracks that go through the CC but not other tracks that aren't biologically plausible. In my fdt_paths.nii.gz file, I see a circular path that crosses to the other hemisphere above the CC from the left preSMA to the right preSMA. These are the paths that I don't want. Maybe it would help if I attach my output files. Please reference the attached files. My dti_FA.nii.gz file was too large so it's not in the attached files. Best, Dana On Thu, Apr 18, 2013 at 2:27 AM, Saad Jbabdi <[log in to unmask]> wrote: > Hi Dana > If you want to exclude tracts that don't go through the CC, then you can > add the CC as a waypoint mask (in addition to the target roi). > > Cheers, > Saad > > On 17 Apr 2013, at 22:20, Dana Wagshal <[log in to unmask]> wrote: > > Hi FSL group, > > I want to complete tractography in an eye-movement network with 16 ROIs. > I'm interested in the pairwise connections between each ROI pair (ex. ROI_1 > -> ROI_2, ROI_1 -> ROI_3, etc) and obtaining a measure of FA as well as the > trajectory between each ROI pair. So I started out with using ROI_1 (ex- > left preSMA) as a seed mask and ROI_2 (ex- right preSMA) as a waypoint. > When I did this there were tracks that went through the corpus callosum as > expected. However, I noticed that there were tracks that went beyond the > right preSMA and tracks that seemed to connect at the very top portion of > the brain not using the corpus callosum. Since I didn't want it to extend > past ROI_2 I also put ROI_2 as a termination mask. This seemed to solve > that problem. However, there still seems to be a good number of tracks that > connect the right and left preSMA that don't go through the corpus callosum > but at a higher level of the brain, which doesn't seem anatomically > possible. > > 1) Why is this happening? > 2) Is there a way to stop this from occurring and to get a track that ONLY > goes from ROI_1 to ROI_2 and vice versa? > > Your help would be greatly appreciated! > > Dana > > > -- > 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 > > > > > > > > > > > > -- -Dana