Volume-based stratification of the cortical surface #251
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This branch is not complete yet, but I created the PR to facilitate discussion about these features and related changes.
This adds volume-based cortical surface stratification to the webgl viewer. This changes the behavior of the 'depth' slider, so that for a selected depth (e.g. depth=0.5), the resulting surface is not halfway between the pial and white matter surfaces, but is instead a surface that has half of the cortical volume above it and half of the cortical volume below it. This obeys "Bok's principle", and much more accurately matches actual cortical layers than the current method.
In preliminary testing volume-based straficiation seems to have a modest effect on the mapping of high-resolution data, such as T1-weighted volumes, but I haven't tested lower resolution functional data. In particular, I found that the new method yields T1w maps that are less confounded by surface curvature than the old method, which suggests that it is indeed more accurate.
Currently equivolume-mode is disabled by default, and can be enabled in a webgl viewer by checking a box labeled 'equivolume'. In my opinion there is no reason to prefer the old distance-based cortical surfaces to the new volume-based surfaces, so I think the default should probably be that it is on, but that can be discussed.
The equation for determining the location of a cortical surface using volume-based sampling comes from this paper: http://www.sciencedirect.com/science/article/pii/S1053811913003480
More information about this technique can also be found here: http://brainvoyager.com/bv/doc/UsersGuide/HighResDataAnalysis/EquiVolumeDepthModelling.html
Edit: many thanks to @kwagstyl for discussions and help with the theory & equations here.