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Published 20 hours ago • verified publisher icon nipreps

Integrate SynthStrip?

Open oesteban opened this issue 2 years ago • 8 comments

Considering the incredible success with MRIQC (@ahoopes SynthStrip is amazing), I think we could consider the integration of SynthStrip here.

oesteban avatar Aug 26 '22 12:08 oesteban

Hi Out of curiosity.... has synthstrip already been implemented? Skimming the release notes, this seems not to be the case. Are there any plans to do this in the near future? Cheers William

WilliamFCB avatar Oct 05 '23 14:10 WilliamFCB

We haven't yet - we are piloting it with MRIQC and on the one hand it is super reliable. But on the other, it is making really hard for people to run MRIQC and not fall into memory errors.

oesteban avatar Oct 05 '23 19:10 oesteban

I understand. Would it be feasible to add it as an extra option so that people can choose? I have been successfully using synthstrip in different pipelines to optimize masks, for example in fixel-based analyses.

WilliamFCB avatar Oct 05 '23 20:10 WilliamFCB

Let's do it "for mp2rage".

On Thu, Oct 5, 2023, 22:33 WilliamFCB @.***> wrote:

I understand. Would it be feasible to add it as an extra option so that people can choose? I have been successfully using synthstrip in different pipelines to optimize masks, for example in fixel-based analyses.

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oesteban avatar Oct 05 '23 20:10 oesteban

Why only for mp2rage? I assume implementation wise at least the -b flag will be made parsable?

WilliamFCB avatar Oct 06 '23 05:10 WilliamFCB