5ttgen: Recommended approach to dealing with white matter hyperintensities (WMHs) for ACT

Hi @NicDC & @cbajada,

Hope you’re both doing well. :slightly_smiling_face:

Yes, exactly. It’s important to reason about them only, but also precisely, in this context.

Both are reasonable choices (what you prefer will depend on your specific application here); in any case avoid them being labelled or treated as GM, because that will force streamlines to terminate in them, i.e. that would also actively “interrupt” regions that can or even should be tracked through.

…so indeed, that’s naturally the pitfall that occurs and should be avoided.

You might want to look into some of the typically available toolboxes for that. Take a look for example in some of our recent works here and here for examples of what we used to segment WMHs. We’ve had success with various toolboxes (e.g. HIST, W2MHS, BIANCA), but you might want to test and evaluate a few to get a feel for what works best on your data.

That might not per se be so bad (it would align with the first option that @cbajada clarified), but you might get unexpected downstream issues if tractography can’t pass through because of other reasons though. The prime reason here would be (sometimes greatly) reduced FOD amplitudes. You’ll have to reduce the FOD amplitude threshold accordingly. This will be challenging in its own right: essentially, no single FOD amplitude threshold might generalise well for both healthy as well as lesioned WM. We actually encountered the same challenge trying to track through glioma’s in this work. There’s no general solution here: we actually somewhat pragmatically reduced the FOD amplitude threshold upon approaching the tumours (and within).

Finally, I just remembered this coming up recently in this topic as well: depending on whether there’s still some false positive GM or even false positive other tissue segmentation nearby the lesions, it might be a good idea to e.g. dilate your lesion segmentations a small bit before employing them as the “5th” tissue (if you’re planning on using them in this way at least). Whatever the streamlines can “hit”, will be used as the rule. This makes it highly sensitive to even small inaccuracies. Extending the “no rule” (“5th” tissue) zone slightly can help to avoid unexpected behaviour nearby.

Cheers & take care,
Thijs

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