khanlab
New atlas from unfoldreg subfields
I've been meaning to incorporate this feature for some time now, and the changes ended up being pretty minimal (ie one new rule) since most of the existing infrastructure (e.g. generic unfolded registration with any metrics, atlas generation with custom metrics) already supports it..
Still a WIP draft PR, as it is only dry-run tested, but I plan to build a HCP UR100 template including myelin as an initial use-case..
- this adds a new form of atlas creation where the subject subfields come from "unfoldreg", i.e. from some existing base atlas (like multihist7), instead of from "native" (manual segmentations).
- a --new-atlas-subfields-from CLI option has now been added to specify either native or unfoldreg
- this supports the use-case of building a new atlas using additional metrics and on populations, the idea being that such an atlas should improve inter-subject alignment
- atlas CLI args have also been renamed/simplified for clarity, adding --new-atlas in front of args that relate to new atlas building..
- dry-run test cases have also been included
- note: behavior for existing atlas creation from native subfields should be unchanged (but you will now need the --new-atlas-from native)
- ~also includes a bugfix from a file I removed that was still needed..~ merged already
Atlas generation is working now, and a newly made hcpUR100myelin template has been generated and pushed to hippunfold-atlases (uses curvature, gyrification, thickness, myelin).. note this atlas must be used with --generate-myelin-map..
I've also confirmed that using a different atlas results in different metric maps, due to differences in the unfolded registration. Will demonstrate this in more detail for the paper..
I'm happy to merge this in, but I was wondering if you're still planning to make a demo for the paper?
Sorry I've been swamped with things haven't been able to bring my attention back to this.. Hoping to get some stuff off my plate this week so I can attend to it..