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Thanks Matt - completely agreed - just one thing to add. If you are using waypoint masks to define a tract, then sometimes your results may look more consistent across subjects if you threshold as a proportion of the total number of samples that made it between the 2 masks rather than the total number sent from the ROI. This number is stored in waytotal.txt. T On 11 Jun 2008, at 03:06, Matt Glasser wrote: > Since I was the one who decided on the threshold in the referenced > paper, I might warn you that it was based on what worked well for > those datasets to exclude low probability voxels that were not of > interest while preserving higher probability voxels that were. I > just completed arcuate tractography on another dataset, and got a > rather different threshold value that seemed to work best 2.0e-6 % > of total samples sent out from the ROIs. One difference between > the two datasets is that my seed space in the below referenced > paper was in diffusion space, whereas in the new study, it is in > structural space. Thus, if the DTI resolution were 2x2x2mm and the > structural resolution were 1x1x1mm, each voxel of DTI space would > correspond to 8 voxels of structural space, and this may be the > cause of the difference. Because probtrackx produces a continuous > probability distribution, there is no “rule of thumb” that allows > you to threshold results from any tract in any dataset at the same > absolute number. I think two things are important: 1) That you use > a consistent percentage of the total number of samples sent out for > each tract across subjects (so that tracts created by larger ROIs, > and thus have more total samples sent out, have higher thresholds) > and 2) That in setting the percentage that you will use, you try a > variety of values and see what seems to produce clean results > showing the pathway of interest without many extraneous pathways > not clearly connected to the ROI but at the same time does not > remove large parts of the pathway of interest (because it is too > high). Tim et al may have further thoughts. You can reduce the > amount of extraneous pathways by carefully choosing your method of > tractography (i.e. the ROIs you use) and using the colors and lines > displays of FSLView to get an understanding of what the diffusion > is doing in your pathways of interest and/or restricting your > pathways to white matter by segmenting a structural image and > turning greymatter and CSF into a “stop” mask. If you use fairly > large ROIs and get pathways of few samples, that may suggest that > any pathway between the regions is either very weak or does not exist. > > Peace, > > Matt. > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf Of Ted Yanagihara > Sent: Tuesday, June 10, 2008 9:41 PM > To: [log in to unmask] > Subject: Re: [FSL] ProbTrack - selecting threshold > > This is a great paper to start with. Be sure to read the > supplementary material for more info on the methods. > > Rilling et al. Nature Neuroscience (2008) vol. 11 (4) pp. 426-428 > http://www.nature.com/neuro/journal/v11/n4/abs/nn2072.html > > Hope it helps! > > ted > > On Jun 10, 2008, at 9:28 PM, Ruth Carper wrote: > > > Hi, > I'd like to use ProbTracks to identify some white matter tracks. Do > you > have any suggestions for selecting a threshold value to define a > tract? > i.e. I have seed and target masks which produce an intervening > tract, but > many of the voxels have very low values (indicating few > streamlines). How > do I select a good cutoff value for what I can be confident is the > real > tract? Any rule of thumb? > > --Ruth >