Hi all,
I’ve been thinking about how to best translate outputs of the Human Connectome Project pipelines into BIDS format, and I’ve come across some issues that point to limitations of the SpatialRef metadata system for dealing with surface data and coordinate systems.
As an example, these outputs include surfaces in fsnative space, and surfaces defining the fsLR template, both of which have straightforward spatial references. But they also include files like the fsnative space pial surface, resampled to the fsLR coordinate system, at some mesh resolution. In this case, the “spatial reference frame” of the surface (ie, the mapping of surface coordinates to a volumetric space and T1 image) is still fsnative, but the coordinates used to define the surface correspond to fsLR. How would this be specified in the BIDS filename/metadata for this surface? Using the density field to specify the coordinate system doesn’t work, because fsLR can still be sampled at multiple densities. The desc field could be used, but this seems inappropriate for such an important property, relating to the definition of the surface coordinate system, and determining correspondence with metric/label images.
This brings up a related issue about metadata for metric and label gifti files. These files are only tied to a coordinate system, not to a specific spatial alignment of that coordinate system. IE, I can attach a metric in fsLR coordinates to either the fsLR pial/etc surface, or to a surface in fsnative space with fsLR coordinates, etc. Since there isn’t an intrinsic spatial interpretation of the coordinates in these files, without attaching them to a surface file, it’s not clear that we should describe these files with a “spatial reference” in the way that we do volume and surface files.
This leads to a straightforward suggestion for a fix, which is to split surface template definition into two fields: spatial reference and coordinate reference. The coordinate reference would specify the topological interpretation of the coordinate system, while the spatial reference would specify the embedding of those coordinates within a specific 3D spatial frame. Surface files would have both a spatial and coordinate reference, while metric/label files would only have a coordinate reference. This would better reflect the metadata needed to interpret each file type, and would enable a natural naming convention for all of the HCP pipeline output surfaces.
Curious what you guys think about these issues and potential solution. It looks like there are some similar ideas on the most recent BIDS RC14 document, although maybe not exactly this.
cc @oesteban, @effigies, @franklin, @satra
cheers,
Ben