How to use 5ttedit -path

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OK, two things:

  • the 5TT image is a 5 volume image, corresponding to GM, DGM, WM, CSF, and pathology (see docs). You’re only showing the first volume, basically saying that there is no GM at that location, but this doesn’t say anything about what tissue type is at that location (WM, DGM, pathology…).

  • if you’ve set this region to pathology using the 5ttedit -path command, then bear in mind that what this does is to instruct tckgen -act to disable all ACT priors – it simply tracks as best it can, the streamline won’t be discarded due to early termination, etc. It does not prevent streamlines from propagating in that region. If that’s what you’re after, it would be simpler to mask out the region altogether from all volumes in the 5TT image (I guess – @rsmith may have better suggestions).

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