[RTM] ENH: Enable brain extraction with NKI template #729
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This was referenced Sep 29, 2017
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If FreeSurfer masks looked good it might be to revisit #431. |
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State of this PR
This PR builds in the infrastructure for using alternative templates, and adds an option to use the NKI template instead of the default OASIS.
Something similar has been done in the @kochalka branch, which suggests that the ability to customize skull-stripping templates is desired by at least some users.
That said, I don't recommend adding NKI as an option without specific user demand or a demonstration that it improves skull-stripping in some cases.
Original text
An attempt to address #701. There was previous discussion of using the NKI template as an alternative to OASIS. In that case, the issue was wrap-around, so it's not clear that we're going to see any improvement here.
I was able to replicate the poor skull stripping locally. Incidentally, the FreeSurfer reconstruction looked great despite that, possibly due to T2 pial surface refinement.
Will report back on skull-strip quality in the morning.