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Hi Ran I had forgotten that there was a bug in the seed-to-target mode in FSL500 and FSL501. You need to download the current version if you want to use seed-to-target. Sorry about that. Cheers Saad On 2 May 2013, at 16:08, Ran Xu <[log in to unmask]> wrote: > Hi Saad, > > I uploaded the data of two cases, including the original data and created "seeds_to_targets.nii.gz". Both of "seeds_to_targets.nii.gz" have the large values, one looks like a spot and one looks like occupying full of whole background. I used this command for case2, similar to the case1 except for the different seed, target and exclusion masks. > 'probtrackx2 -s %s -m %s --seed=%s --targetmasks=%s --waypoints=%s --stop=%s --dir=%s --avoid=%s --onewaycondition -S 100 -c 0.7 --os2t --opd',sname, mname, seed_name4, tar_name4,tar_name4,tar_name4,result_path4,excl_mask > > Please let me know if you find something. > Thank you so much. > > Ran > > > On Thu, May 2, 2013 at 3:16 AM, Saad Jbabdi <[log in to unmask]> wrote: > Hi Ran > > No you can keep the --opd option. > > I am not sure what is happening here. I will need to look at your data to see if I can replicate it. I have sent you a link to an upload website. Please follow the instructions on that link. > > Cheers > Saad > > > On 1 May 2013, at 17:44, Ran Xu <[log in to unmask]> wrote: > >> Hi Saad, >> >> Thanks for your reply. I didn't use the --pd option, instead I used --opd option. Should I delete --opd option? I also want to see the fdt_paths.nii file. >> >> Thanks. >> Ran >> >> >> >> >> >> On Wed, May 1, 2013 at 11:32 AM, Saad Jbabdi <[log in to unmask]> wrote: >> Hi - you are probably using the --pd option (distance correction). You need to turn that off if you want streamline counts. >> >> Cheers >> Saad >> >> On 1 May 2013, at 17:14, Ran Xu <[log in to unmask]> wrote: >> >>> Dear FSL experts, >>> >>> I used probtrackx2 with 5000 streamlines for each seed voxel to create the "seeds_to_targets.nii" file. When I loaded the "seeds_to_targets.nii" file, I found some values in it are more than 5000, even reaching a value like 4488952, it's so large. Is it right? Is there a possibility that the value also includes the number of streamlines from other seed voxels passing through this seed voxel? How could I get this voxel's real streamline number because I wanna know the total connection number. >>> Another "seeds_to_targets.nii.gz" file gave me some Nan or Inf values. Is it ok if I just ignore these numbers? >>> >>> Thank you so much, >>> Ran >> >> -- >> 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 >> >> >> >> >> >> >> >> >> >> >> >> > > -- > 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 > > > > > > > > > > > > -- 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