Thanks a lot for your reply, much appreciated. That's good to know. I used the matrix1 option with 82 seeds, so I don't know what you mean with inclusion/exclusion mask. This is what I used:
/Applications/fsl/fsl/bin/probtrackx2 --network -x /Volumes/DTI/PROBTRACKX/HC005/masks.txt -l --onewaycondition --omatrix1 -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01
--distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /Applications/fsl/fsl/subjects/preprocessed/HC/005.bedpostX/merged -m /Applications/fsl/fsl/subjects/preprocessed/HC/005.bedpostX/nodif_brain_mask --dir=/Volumes/DTI/PROBTRACKX/HC005
Is it ok in my case to normalise by the values in the waytotal file?
Thanks again for your help.
André