Use subject specific BOLD template for T1w coregistration

[chrisgorgo]

Such template would:

• improve within subject overlap
• improve coregistration with T1w

How to create it:

• If SBRefs are present use them exclusively
• If SBRefs are not present use reference_images from all runs

Affine unbiased coregistration seems a good method for creating such template.

[oesteban]

This idea would require susceptibility distortion correction, otherwise the references are likely to have different realizations of distortion and the fused reference will be smoother than the individual cases.

What did you mean by affine unbiased coregistration?

[oesteban]

Rescued from the duplicate issue (Chris M.):

Thinking about what's involved in this:

• Single workflow that takes all BOLD series
• Each series needs to be SDC unwarped
• Resulting reference files then merged with StructuralReference, and (EPI -> mean EPI) transform saved
• Mean EPI aligned to T1w image

This will involve a fairly major refactor from the current, isolated processing of each BOLD series. One problem with this approach is that you can get different results based on whether your analyze all tasks or just a subset in the same process.

However, if we took an EPInorm approach, then there's a common space to which all EPIs are registered that doesn't depend on which subset of tasks have been specified.

WDYT?