Hi Saad,
I'm very grateful for your answer, not only giving a solution to my issue but taking time to write code i could use to solve it entirely.
Also great anticipation about the stopping masks, i didn't use them and will re-run the tractography with the target ROIs used also as stopping masks.
I prefer not to use the --network option as i believe the tract directions can only be well defined in white matter.
Thanks again for your help,
Michael
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