External Email - Use Caution
From: Timothy Coalson <tsc...@mst.edu> Reply-To: Timothy Coalson <tsc...@mst.edu> Date: Monday, October 28, 2019 at 8:21 PM To: "Glasser, Matthew" <glass...@wustl.edu> Subject: Re: FW: [Freesurfer] Mapping coordinates from sphere file to ?h.white That is not a sphere of fs_LR coordinates (in fact, "fs_LR coordinates" is not really a meaningful phrase). That sphere's per-vertex coordinates are specifically intended to spatially line up our fs_LR atlas data to fsaverage atlas data on the fsaverage atlas sphere, because this is the information needed to resample between the atlases. It has the same number of vertices as fs_LR surfaces because it needs to know the target location on the fsaverage atlas sphere for every fs_LR vertex. The inflation of an anatomical surface to a sphere is a tricky process, as the surface can easily fold back over itself (which would encode a non-invertible transformation). The path the vertices took to get to a sphere is neither recorded, nor particularly important to anyone not working on the implementation details of the inflation. The endpoint of the process, the spherical surface, is the only goal, the displacement vectors between them are not useful to surface operations (since the data is tied to the vertices, and all the vertices still exist in the sphere (just at new coordinates), it is trivial to use the same data "on" either the sphere or anatomical surfaces). These spherical surfaces are only used to do registration and resampling (which does not involve any kind of warp of anatomical coordinates), after which the data is used with anatomical surfaces (which always maintain the original shape and size even when resampled), because spatial processing should be done on brain-shaped geometry, not on spheres. It is unclear to me what you intend to use the surface you described for, and I don't know what the .x5 format is. The surface resampling weights are fairly easily derived from the correct pair of spheres, and resampling does not involve any kind of spatial displacement. Tim From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Oscar Esteban <p...@oscaresteban.es<mailto:p...@oscaresteban.es>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, October 28, 2019 at 6:58 PM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Mapping coordinates from sphere file to ?h.white External Email - Use Caution Dear experts, In the context of the BIDS transforms extension and the ".x5" format we chatted about in the workshop we made in March at MIT, we are addressing the following question. We have a sphere of fsLR coordinates in fsaverage space (e.g., https://github.com/Washington-University/HCPpipelines/blob/master/global/templates/standard_mesh_atlases/resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.59k_fs_LR.surf.gii - but the question extends to the right hemisphere and also resolutions other than 59k). We want to expand this sphere to the fsaverage's white surface (lh.white, in this example). Since coordinates on the fsLR sphere don't match any of fsaverage{,3,4,5,6}'s coordinates, we wonder whether FreeSurfer stores somewhere/somehow the analytical transform of this mapping. In other words, how one would map arbitrary coordinates on the surface to a particular fsaverage's white (or midthickness, or pial, etc.) surface. Otherwise, I guess I would pick fsaverage's surfaces (i.e., 7th degree icosahedron), and interpolate the displacement vectors that start at each sample on the surface and end at the corresponding location of that vertex index of the destination surface (lh.white for the example above). Is there any tool that actually does the _inverse transform of the surface-to-sphere mapping_? Thanks very much. Regards, Oscar -- ___________________________ Oscar Esteban, Ph.D. Postdoctoral Fellow, Poldrack Lab Stanford University +1 (650) 733 33 82 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. 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