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Alternatively, you can also plot FA against (expected) distance from seed as you would do in deterministic (I sent you the scripts to do that Derek!) Saad. On 21 Oct 2010, at 16:46, Matt Glasser wrote: > Hi Derek, > > I did option number 2 to get around the thresholding problem (it is very hard to figure out exactly how to define a threshold in a principled way, see numerous discussions on the list about this). I did it on whole ROI results, though, which is not what he is asking for. I did this on symmetrically tracked results from two ROIs, which should only bias measurements towards tracts that are between the ROIs. If you used single ROIs or asymmetric tracking (seed à waypoint) you would probably bias your results towards the seed ROI. As compared to thresholding the paths at some value, I found that I got higher FA values from this method, likely because high probability voxels tend to be in core white matter. Unfortunately, this was for a grant submission so I don’t have a citation for this method. > > Peace, > > Matt. > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Derek Jones > Sent: Thursday, October 21, 2010 10:37 AM > To: [log in to unmask] > Subject: Re: [FSL] Probtrackx: Vector Output? > > > I'd also like to ask - for those that have employed such an approach: > > 1) Do you choose a statistical threshold on the ProbTrackX result - and then take the average metric from all remaining voxels in the tract (i.e. 'significant' tracts). If so - what threshold do you use? > > 2) An alternative approach would be to weight the metric by the 'probability' of the voxel being part of the tract, such that those voxels that are intersected most frequently will have a proportionately larger contribution to the average. > > ...and does this bias the measurements to the FA / RD / ADC of the tract that is closer to the seedpoint? > > Thanks in advance to anyone that replies > > Derek > > ______________________________ > Derek K Jones > CUBRIC > School of Psychology > Cardiff University > Park Place > Cardiff > CF10 3AT > Tel: +44 (0)29 2087 9412 > Fax: +44 (0)29 2087 0339 > Web:http://www.cf.ac.uk/psych/contactsandpeople/lecturing/jones-derek-prof-overview_new.html > http://cubric.psych.cf.ac.uk/people/derek-jones/ > > > >>> Bryan Benson <[log in to unmask]> 10/21/2010 3:26 PM >>> > Hello FSL experts, > I'm wondering if any of you have found a way to export the results of probtrackx as paths, rather than as images. I'm interested in looking at structural connectivity in a voxelwise manner; e.g. given two voxels, looking not only at the relative probability of a connection, but also at the average microstructural measures (FA, RD, ADC) of the paths found. This should be possible (since the paths must originally be calculated in these terms) and given the popularity of this approach, I figured someone has probably done it already with FDT. > Just using the fdt_paths output as a mask won't help to answer the question because I want to examine compare voxels within seed masks, rather than across them (and running each voxel individually as a seed would be very inefficient). > Thank you very much! > Bryan -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad