Hi @rsmith
Thanks for your answer. We checked some of the stuff you mentioned and had a look at the mask images. The mask images look fine, with the mask not going over the brain boundaries.
It might be relevant for the issue that we have single shell data (see: Error in mtnormalise with problems with gmfod in dwi2fod).
We also checked if using 5ttgen hvsv makes any difference, but we could see any (left hvsv, right fsl):
Is the problem in the data (might due to being single shell)? Or could the problem lie in the calculation of the tracks themselves with a too high threshold for where to create tracks, maybe?
Thanks again!
Best,
Joshua