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Hi Saad, Sorry for being thick. But just to be clear, if I want to compute the strength of connection from a seed mask to a target mask then should I only use the sum of counts from the appropriate column of "matrix_seeds_to_all_targets"? Cheers, Jackson ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Saad Jbabdi [[log in to unmask]] Sent: 15 August 2013 16:53 To: [log in to unmask] Subject: Re: [FSL] probtrackx2, waytotal > num. of samples Yes that's correct. On 15 Aug 2013, at 16:47, Jackson Smith <[log in to unmask]<mailto:[log in to unmask]>> wrote: Thanks again. I see that I don't fully understand what waytotals are. Just to be clear, what precisely are the values contained in the"matrix_seeds_to_all_targets" file? These are only counts, not waytotals? I guess that rejected streamlines are never counted? Best, Jackson ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Saad Jbabdi [[log in to unmask]<mailto:[log in to unmask]>] Sent: 15 August 2013 16:38 To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] probtrackx2, waytotal > num. of samples Aha! That makes much more sense. I was under the impression that streamlines terminate as soon as they reach a target. I take it that streamlines simply run to their full extent, and that the waytotal is increased for any target areas that it happens to touch? If a streamline passes through more than one voxel of the same target then is it counted as passing through that target more than once? No, the waytotal number is the number of streamlines that were not rejected. It does not matter how many voxels a streamline crossed, it is only counted once, if at all counted, in the waytotal. Lastly, is there a way to make streamlines terminate the moment they make contact with a target? Yes, you can set your target masks as stopping masks. Saad Thank you, Saad. Jackson ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Saad Jbabdi [[log in to unmask]<mailto:[log in to unmask]>] Sent: 15 August 2013 12:49 To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] probtrackx2, waytotal > num. of samples Hi The "matrix_seeds_to_all_targets" output text file contains a matrix with as many rows as there were voxels in the seed mask, and as many columns as there were target masks. Running along one row of values should be the waytotal from one seed voxel to each target mask, in turn. Therefore, the sum across columns should always be less than or equal to the value given for "-P", the number of streamlines generated per voxel. Alternatively, the sum across rows should be the waytotal from the entire seed mask to each target mask. No, that is only true if each streamline goes through only one or zero targets. If streamlines pass through more than two targets, then the sum across columns can be higher than waytotal. Cheers, Saad However, I find that the sum across columns is sometimes greater than the value that I gave for "-P". Is there something I've misunderstood about what the values in "matrix_seeds_to_all_targets" mean? Kind regards, Jackson Smith -- 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> -- 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> -- 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>