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EPInorm to replace EPI->T1w->MNI registration #620

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effigies opened this issue Jul 28, 2017 · 8 comments
Open

EPInorm to replace EPI->T1w->MNI registration #620

effigies opened this issue Jul 28, 2017 · 8 comments

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@effigies
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@effigies effigies commented Jul 28, 2017

http://onlinelibrary.wiley.com/doi/10.1002/hbm.23737/full

Supersedes #253, and may make ultimately replace SyN-based susceptibility distortion correction (#496/#544).

@chrisgorgo

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@chrisgorgo chrisgorgo commented Jul 28, 2017

When you have read the paper carefully could you list the pros, cons, and risks (things to look out for) of replacing syn based SDC with EPInorm?

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@chrisgorgo chrisgorgo commented Jul 29, 2017

It might be also interesting to think about this in terms of a new optional target template EPIMNI.

@oesteban

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@oesteban oesteban commented Jul 29, 2017

That target would not be the same as MNI but specifying a resolution?

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@chrisgorgo chrisgorgo commented Jul 29, 2017

The original paper used an EPI template instead of a T2w one (which we would have to use if we wanted to stick to 2009c) https://twitter.com/vdcalhoun/status/890217862010355713

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@effigies effigies commented Jul 29, 2017

Looking at the EPI/T2 templates in SPM12, these at least are very similar; EPI.nii basically looks like a skull-stripped version of T2.nii. I haven't looked at the 2009c ones, but at a first pass, I'd think skull-stripping the T2w template and rescaling to match the EPI (as we do in creating the inverse T1w image) would get us to a similar starting point as EPInorm.

I'd think an EPIMNI target would just be the same as MNI... I'm not sure what you have in mind, unless it's to say don't bother resampling the anatomical to the MNI space. (Which, I'd think we wouldn't bother doing if we use EPInorm, unless we want to have a warp back to subject-native space.)

I feel like a major test of the (EPI -> MNI -> T1w) pipeline replacing SyN-SDC would be surface-sampling.

I'll give the paper a close reading and share my notes.

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@chrisgorgo chrisgorgo commented Jul 29, 2017

I see - thanks for doing this comparison.

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@oesteban oesteban added this to Watching in 1.3.0 Mar 1, 2018
@oesteban oesteban moved this from Watching to To do in 1.3.0 Jul 31, 2018
@oesteban oesteban moved this from To do to In progress in 1.3.0 Oct 18, 2018
@oesteban oesteban removed this from In progress in 1.3.0 Jan 12, 2019
@oesteban oesteban removed this from the 1.1.0 milestone Jan 30, 2019
@oesteban oesteban added this to To do in pipelines Mar 6, 2019
@franklin-feingold franklin-feingold moved this from To do to Issues B-list in pipelines May 6, 2019
@oesteban oesteban added this to the 2.0.0 milestone Jul 11, 2019
@effigies effigies moved this from Issues B-list to Issues A-list in pipelines Sep 30, 2019
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