Confirmation of single-shell FBA pipeline use

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Hi there, just wanted to follow up on this. I saw this post: Fixel-Based Analysis on single shell data

saying that one should probably use the single shell pipeline after generating the FODs and response functions because the step with mtbin (mtnormalise now, I’m assuming) requires 3 tissue CSD responses. I only have b=0 and b=3000 data, so should I be using the single tissue pipeline after dwiresponse and dwi2fod?

Best,

Ana

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Hi Ana,

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 dwiresponse and dwi2fod?

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 dwibiascorrect and dwinormalise group even in the single-shell WM+CSF case; it would be worth finding and reading such discussion(s).

mtbin (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?

Cheers
Rob