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Show a big-fat warning when a brain mask is not provided #107

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oesteban opened this issue Dec 9, 2022 · 2 comments
Open

Show a big-fat warning when a brain mask is not provided #107

oesteban opened this issue Dec 9, 2022 · 2 comments
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@oesteban
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oesteban commented Dec 9, 2022

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
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arokem commented Dec 9, 2022

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

@oesteban
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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.

@oesteban oesteban added this to the 0.1.6 milestone Apr 3, 2024
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