I shifted your question to a new topic since it isn’t specific to the title of the earlier thread (on relative AFD in GM vs. WM in single-shell low-b-value data).
I only have b=0 and b=3000 data, so should I be using the single tissue pipeline after
Given what you have is single-shell data by definition, we would have no choice but to direct you to the single-tissue pipeline; though you would need to be “using” that pipeline before
dwi2fod rather than after, given that’s a key point of divergence of the two pipelines. Further, the b=0-based global intensity normalisation step is still included in the suggested single-tissue pipeline, as opposed to the multi-tissue-based intensity normalisation in the suggested multi-tissue pipeline, meaning that being faithful to the former requires such a decision prior to even
dwi2response. Though there has been discussion about whether using
mtnormalise is preferable to the combination of
dwinormalise group even in the single-shell WM+CSF case; it would be worth finding and reading such discussion(s).
mtnormalise now, I’m assuming)
Correct; but is your reference to
mtbin based on your own memory of such, or is there a lingering reference to it somewhere that we need to update?