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nipreps / eddymotion

Open-source eddy-current and head-motion correction for dMRI.
https://nipreps.org/eddymotion
Apache License 2.0
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Show a big-fat warning when a brain mask is not provided #107

Open oesteban opened 1 year ago

oesteban commented 1 year ago

With the development of #91, it has become clear that we don't want to be fitting models in background pixels, nor have the background be considered by the cost function of ANTs.

Therefore, eddymotion should be very reluctant to go ahead without a brain mask.

Incidentally, I believe can easily include SynthStrip into dMRIPrep and then dilate that mask so that distortions do not cause cropping of the brain.

WDYT?

arokem commented 1 year ago

I ❤️ synthstrip and I think that's a great idea. We should also give the option to provide masks from other pipelines.

oesteban commented 1 year ago

Correct, we don't want to mess with how the user calculates masks - eddymotion should just trust the user is doing the right thing on this aspect.