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Dear Saad thank you a lot for answering.So I will use the seed_to_target files and divide each one for the corresponding column of the matrix_seed_to_targets . Best regards Francesco Sammartino On Jul 31, 2016 4:34 AM, "Saad Jbabdi" <[log in to unmask]> wrote: > Hi - you need to divide by the number of samples that connect to your > targets, not the waytotal (which may count other streamlines unless your > target masks are also used as waypoint masks). > > Cheers, > Saad > > > > > On 29 Jul 2016, at 21:59, Francesco <[log in to unmask] > <[log in to unmask]>> wrote: > > Dear FSL list > > I'm sorry if perhaps this question has already been asked in the past > years but I am not able to understand if I'm doing my analysis correctly. > > I want to analyze the connectivity in 1 subject of a 2mm radius mask in > the accumbens.Voxel size of the diffusion images is 1.5mm isotropic. > > I have specified masks from the cortical parcellation of the left > hemisphere as classification targets in probtrackx (similar to what is done > here http://sburns.org/2014/05/03/cortical-tractography-recipe.html). I > summed the values in the columns of matrix_seeds_to_targets and divide by > the waypoint value to obtain a proportion of tracks reaching each cortical > target . > > At this point some of the values is really low (they are all below one) > .Am I doing it correctly? > > Thanks any suggestion is much appreciated. > > >