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Also, you can use a region as a waypoint, termination, and classification target at the same time. That way, you can get your quatitative comparisons from the seed_to_target files, and dissect your connection via waypoint/termination to check that it is anatomically reasonable. Cheers, Saad. On 25 May 2009, at 05:48, Matt Glasser wrote: > You might be better served by running seeds to targets mode using > each of > your regions as a seed with the other two as targets. This will > record the > actual number of streamlines that go from each seed to each target, > which > will allow you to make quantitative comparisons between the > strengths of > each pathway. > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf > Of Michael Scheel > Sent: Sunday, May 24, 2009 10:46 PM > To: [log in to unmask] > Subject: Re: [FSL] question re probtrackx network mode > > Hi Saad, many thanks for the clarification - I see now why my > suggestion makes little sense. > > Regarding my study - I tried the termination masks but realized this > is not what I want to do. So here is what I want to do: > > I have Region A, B and C. I want to show connections between > A and B, > A and C, > B and C (which I hope are not there according to the hypothesis) > > I'd like to also compare the connection strengths/probabilities for > these connections in a number of subjects. > > Network-mode will give me Connections that pass through the regions, > but I want them to end there. > Termination masks will give me all connections from one region, > including those that terminate in the target region - I want only > those that terminate. > Waypoint masks again will give connections that pass through. > Exclusion masks is not what I want. > > So I'm a bit lost and start to wonder if that's what I want is a > reasonable thing to do, or not? If it is reasonable, which I still > hope - how would you suggest to do that? > > Thanks, Michael > > > On 24-May-09, at 12:36 PM, Saad Jbabdi wrote: > >> Hi Michael, >> >> On 24 May 2009, at 19:07, Michael Scheel wrote: >> >>> Hi Saad, thanks for the answer. Some questions just to make sure >>> that I understood correctly. >>> >>> I've often come across the symmetric mode (---mask2) in the >>> discussions and I was assuming that this is something like: >>> >>> Track from RegionA to RegionB AND from RegionB to RegionA - only >>> those tracts survive that fullfill both conditions. From your answer >>> I understand that they don't necessarily have to take the same way. >>> However - wouldn't that be a strong confirmation of the certainty of >>> the tract travelling this route? I guess depending on seed and >>> target chances are sometimes low that one sample from AtoB has a >>> counterpart BtoA and one would need a huge sample number to find >>> those. One would have to store for every sample of seed region A the >>> "voxelway" and then compare this with the table of voxelways from >>> regionB. I guess the problem is how to visualize the results of this >>> - hower just an idea. >> >> >> There is no theoretical reason for accepting only sample tracts that >> take the exact same route both ways. Remember: in probtrackx, we are >> building a (spatial) histogram of connections using sampling. Each >> sample is a random draw from that distribution. So, even if the >> distribution that represents A->B is the exact same distribution as >> B- >>> A, there is no reason why the samples should be the same.. >> >>> >>> >>> My question really is for the symmetric mode. Does this show (as in >>> network-mode) connections from A that pass through B AND connections >>> from B that pass through A. Or is it connections from A that end in >>> B AND from B that end in A. >> >> Network mode is exactly the same thing as symmetric mode, but >> extended >> to more than two regions. I.e. if you use two regions in network >> mode, >> you get the same answer as two masks symmetric. >> The samples that are kept are the ones that pass through the target >> regions (as opposed to "end in"). >> >> >>> >>> >>> Another question re the network mode: >>> You said: >>>> It will show you an overlay of the following three distributions: >>>> . connections from A that pass through either B or C >>>> . connections from B that pass through either A or C >>>> . connections from C that pass through either A or B >>> >>> Is there an option of tracking: >>> . connections from A that end in either B or C >>> . connections from B that end in either A or C >>> . connections from C that end in either A or B >>> I guess I could use the target mode for every combination and >>> overlay the results - correct? Is there already an option or script >>> to automate this? >> >> You are probably thinking of using termination masks. Unfortunately, >> you cannot use the seeds as terminations in network mode. You will >> need to run probtrackx several times. >> >>> >>> >>> >>> Thanks a lot, Michael >>> >> >> Cheers, >> Saad. >> >>> >>> On 24-May-09, at 2:45 AM, Saad Jbabdi wrote: >>> >>>> Hi Michael, >>>> >>>> On 23 May 2009, at 21:56, Michael Scheel wrote: >>>> >>>>> Hi fsl-gurus, >>>>> >>>>> I have 2 questions re the probtrackx network mode: >>>>> >>>>> Say I have a Region A, B and C defined as masks and enter them as >>>>> Multiple seed masks. >>>>> What connections will be shown to me: >>>>> 1) Any connections between A and B, A and C, B and C or 2) just >>>>> connections that connect all of them, i.e. A-B-C, A-C-B and B-A-C. >>>> >>>> neither exactly 1) nor exactly 2). >>>> It will show you an overlay of the following three distributions: >>>> . connections from A that pass through either B or C >>>> . connections from B that pass through either A or C >>>> . connections from C that pass through either A or B >>>> >>>> >>>>> >>>>> >>>>> Assuming it is (1), and looking only at connections between A and >>>>> B. >>>>> As I understand from previous discussions, tracking samples are >>>>> send >>>>> from A to B and B to A and only those that reach their target in >>>>> both conditions 'survive'. >>>>> What I'm wondering about is what are the constraints regarding >>>>> that: >>>>> Does the sample has to go the exact same voxelway to be found >>>>> valid >>>>> or is it rather an overlay where voxels survive that were passed >>>>> from either direction, i.e. at least one sample passed from AtoB >>>>> AND >>>>> BtoA. >>>> >>>> It is the latter. A tract survives if it reaches its target, >>>> regardless of the route it has taken. >>>> >>>> Cheers, >>>> Saad. >>>> >>>> >>>>> >>>>> >>>>> Thanks, Michael >>>>> >>>> >>>> -- >>>> Saad Jbabdi >>>> Oxford University FMRIB Centre >>>> >>>> JR Hospital, Headington, OX3 9DU, UK >>>> +44 (0) 1865 222545 (fax 717) >>>> www.fmrib.ox.ac.uk/~saad >>> >> >> -- >> Saad Jbabdi >> Oxford University FMRIB Centre >> >> JR Hospital, Headington, OX3 9DU, UK >> +44 (0) 1865 222545 (fax 717) >> www.fmrib.ox.ac.uk/~saad > -- Saad Jbabdi Oxford University FMRIB Centre JR Hospital, Headington, OX3 9DU, UK +44 (0) 1865 222545 (fax 717) www.fmrib.ox.ac.uk/~saad