Enable using templates other than MNI

yeatmanlab / pyAFQ

Automated Fiber Quantification ... in Python

http://yeatmanlab.github.io/pyAFQ/

BSD 2-Clause "Simplified" License

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Enable using templates other than MNI #170

Open jyeatman opened 4 years ago

jyeatman commented 4 years ago

For researchers working with infant data we should make it easy to switch out the MNI template for pediatric templates. If a different template is selected, then the ROIs and probability maps need to be transformed from MNI -> custom template

arokem commented 4 years ago

This is already implemented through the reg_template key-word argument (e.g., here), but it would be good to test this with some real data. Do you have a pointer to a pediatric template we could use to try this out?

jyeatman commented 4 years ago

One other step we might need to include. If someone supplies another template then we need to warp the template ROIs from the MNI template to the supplied template

arokem commented 4 years ago

Oh yes - you're right. I missed that.

Let me see that I understand what would need to happen:

Register custom template to MNI template (affine? non-linear?)
Move waypoint ROIs and probability maps to the custom template.
Use custom template and moved waypoint ROIs, instead of default.

Would that cover everything?

jyeatman commented 4 years ago

yes exactly. Probably doing this with affine + sym. Affine would probably be fine. But I also don't see a reason not to use the "optimal" registration that you already implemented. Though one issue is that the contrast in baby brains is a bit crazy. So in that sense affine might actually be ideal