Hi Can you post the exact command lines you used for the three runs? Saad On 15 Mar 2014, at 22:38, Longchuan Li <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear FSL experts I have a question regarding the symmetrical tracking in probtrackx2. I have two ROIs: one is a subcortical volumetric mask (sub_vol_mask) and another is a cortical surface-based mask (cor_surf_mask). Now I want to perform a symmetrical tracking between the two ROIs. I first performed probtrackx2 without any option, just put the two into a seed mask text file and got some results that are quite reasonable to me (run1). I then tracked them using --omatrix1 option (run2) and I finally ran probtrackx2 again using "--network" option without "--omatrix1" (run3). I got the following results: (1) run1: a pathway seemly connecting the two ROIs, with only *one* waytotal number. (2) run2: a pathway and a waytotal *identical* to that in run1, but with extra files fdt_matrix1.dot. (3) run3: an empty pathway file and a waytotal with two zeros in it. I am a little confused and don't know why I got the result in run3, as I read previous posts saying the "--network" is the correct flag for such analyses. I wonder whether other users have reported similar issues. Any information will be greatly appreciated! Longchuan -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi<http://www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi>