Integrate SynthStrip?

[oesteban]

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

[WilliamFCB]

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

[oesteban]

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.

[WilliamFCB]

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.

[oesteban]

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. — Reply to this email directly, view it on GitHub <#299 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAESDRRTC5OIVCTMMRZZG3LX54KP5AVCNFSM57WTAAR2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZUHE3DAMJQHE2A> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[WilliamFCB]

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

[margokersey]

Hi there, I was curious if there are any updates on incorporating SynthStrip as an option in smriprep? I couldn't find information in the documentation. Thank you!

[oesteban]

Why only for mp2rage?

That would be the "official" use-case. When enabled, a warning stating that using SynthStrip on standard MPRAGE/SPGR images can be done at your own risk because it deviates from the 'official' smriprep workflow.

Eventually, I can see how SynthStrip will totally replace the atlas-based extraction in the long term.

[oesteban]

Hi there, I was curious if there are any updates on incorporating SynthStrip as an option in smriprep? I couldn't find information in the documentation. Thank you!

No progress for the moment, unfortunately. We'd be glad to receive the contribution from someone new ;)