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Hi With this option, there is not a single threshold to set. For a detailed explanation, see a previous post: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=fsl&D=0&1=fsl&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=209265 In general we don't recommend this, but if you want to constraint tracking by setting a specific FA threshold, then you can create a thresholded FA mask (e.g. using fslmaths) and use that as a brain mask in probtrackx. Cheers Stam On 18 Dec 2013, at 10:03, [log in to unmask] <[log in to unmask]> wrote: > Hi, > I would like to ave some more information about the flag "use fractional > anisotropy to constrain track". in the FSL website I found only: > > "Use this option if you want the fractional anisotropic volumes (stored in > merged_f<i>samples) to influence the tractography. > The tracts stop if the anisotropy is lower than a random variable between 0 > (low anisotropy) and 1 (high anisotropy)." > > But what is the value of this random variable and is there a way to set or > change it? > > In what cases is it suggested to use this option? > > Thanks, > Marica.