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I wouldn't recommend using that as you asked to do something different (which I explained how to do). Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of romain quentin Sent: Thursday, April 07, 2011 4:45 AM To: [log in to unmask] Subject: Re: [FSL] option: fa constrain tracts in probtrack I am referring to the option in probtrack : "use anisotropy to constrain tracking". Thanks 2011/4/6 Matt Glasser <[log in to unmask]> Which method are you referring to? Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of romain quentin Sent: Wednesday, April 06, 2011 8:46 AM To: [log in to unmask] Subject: Re: [FSL] option: fa constrain tracts in probtrack Thank you for your reply. However, I do not really understand in which case the fiber stop. is there a place where I can get more information about this option? Is it better to use this option instead of a mask of FA to 0.15 or 0.2? Is it normal that sometimes I get more fiber with this option than without. Thank you very much Romain 2011/4/5 Matt Glasser <[log in to unmask]> If you want to constrain using FA of 0.15, do this: fslmaths <FA> -thr 0.15 -bin -sub 1 -mul -1 <stopmask> And then use <stopmask> as a stopmask in probtrackx. Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Saad Jbabdi Sent: Tuesday, April 05, 2011 1:06 PM To: [log in to unmask] Subject: Re: [FSL] option: fa constrain tracts in probtrack Hi - this option is the probabilistic version of an FA constraint. It will stop tracts with some probability that is dependent on the partial volume fraction of the fibre direction that has been selected at the last step. Saad. On 5 Apr 2011, at 15:57, Romain Quentin wrote: > Hello, > I want to constrain the FA when i launch probtrack at 0.15. > I do not know what value is using the option "use anisotropy to constrain tracking"? > Does anyone know how this option works? > Thanks > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad>