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pyAFQ pipeline uses 0 FA as seed threshold? #563

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arokem opened this issue May 5, 2023 · 1 comment · May be fixed by #571
Closed

pyAFQ pipeline uses 0 FA as seed threshold? #563

arokem opened this issue May 5, 2023 · 1 comment · May be fixed by #571

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@arokem
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arokem commented May 5, 2023

Seed threshold is set to 0 here:

https://github.com/PennLINC/qsiprep/blob/master/qsiprep/data/pipelines/pyafq_tractometry.json#L20

Does that mean that pyAFQ uses FA=0 as default threshold for the seed mask? It definitely looks like it from data we've looked at.

Or does it propagate a binary WM mask from the previous qsiprep steps? Is there some way to make that the default behavior?
This was referenced May 12, 2023
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@arokem
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arokem commented May 12, 2023

I have been set right by @36000 : when the seed_mask is set to an empty string, that means that we use the default behavior in pyAFQ, which is FA with 0.2 threshold, which is a totally reasonable thing to do. Nevertheless, #571 will change the default to use the already-generated WM probability mask.

@arokem arokem closed this as completed May 12, 2023
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