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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