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Hi Saad, do they just have to pass one voxel within the ROI or through the entire ROI? Thanks & cheers, Andreas Von: Saad Jbabdi <[log in to unmask]> Antworten an: FSL - FMRIB's Software Library <[log in to unmask]> Datum: Mittwoch, 5. Februar 2014 11:41 An: <[log in to unmask]> Betreff: Re: [FSL] probtrakx_seed_target-multiple_mask Hi In network mode, the two ROIs are considered in turn as seed and ³waypoint² respectively. Therefore, all streamlines that do not pass through the ROIs will be rejected - if the ROIs are set as ³targets², then streamlines that do not pass through the targets will still be included in the fdt_paths output, but discarded from the seed_to_target counters. Cheers Saad On 5 Feb 2014, at 08:06, [log in to unmask] <[log in to unmask]> wrote: > Hi, > > I am running Probtrackx using two ROIs (ROI_1, ROI_2) and I am interested in > the global connectivity between these two regions. So what I need is the > global > number of fibers which start from ROI_1 and reach ROI_2 and the same in the > opposite direction (from ROI_2 to ROI_1). What I see in that there are two > different ways to proceed: > > - Run probtrackx in multiple mask mode, using my two ROIs as masks; > > - Run probtrackx in seed to target mode, using as seed ROI_1 and as target > ROI_2 and the same in the opposite direction (seed ROI_2 and target ROI_1). > > These two methods give very different results. Could you suggest me what is > the best way to proceed? > > Thank you in advance! -- 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>