EPInorm to replace EPI->T1w->MNI registration

nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

https://fmriprep.org

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

Open effigies opened 7 years ago

effigies commented 7 years ago

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 commented 7 years ago

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?

chrisgorgo commented 7 years ago

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

oesteban commented 7 years ago

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

chrisgorgo commented 7 years ago

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

effigies commented 7 years ago

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.

chrisgorgo commented 7 years ago

I see - thanks for doing this comparison.

chrisgorgo commented 6 years ago