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Hi Jon You can estimate tractography-induced streamline density with probtrackx2. There is lots of documentation and tutorials in the FSL course material to give you a first overall idea. E.g. look at the FDT practicals at: http://fsl.fmrib.ox.ac.uk/fslcourse/ Notice that you cannot really get “tract density” strictly speaking, but you can estimate surrogates of it. Cheers Stam On 6 Oct 2015, at 18:43, Jon Anderson <[log in to unmask]> wrote: > Dear FSL experts, > I want to calculate tract density ( number of DTI fibers comprising the tract - in other words the number of distinct tracts that pass through the manually constructed sets of ROIs) . I have run Bedpostx and I got the following files as an output of the process: > > dyads1.nii.gz > dyads2.nii.gz > mean_f1samples.nii.gz > mean_f2samples.nii.gz > merged_f1samples.nii.gz > merged_f2samples.nii.gz > merged_ph1samples.nii.gz > merged_ph2samples.nii.gz > merged_th1samples.nii.gz > merged_th2samples.nii.gz > > Please any help is highly appreciated. > > Thanks > Jon