No, we do not have a precomputed file of geodesic distances, we compute them on the fly in any operation that needs them. Using the -surface-geodesic-distance command on each vertex of interest is certainly one way to find these distances, and may be the best available way depending on the language or tools you intend to use for further analysis. However, you should use individual surfaces when processing an individual's data, as averaging the surfaces of a group of subject results in smoothing out folding patterns, with more smoothing in higher variability areas, which changes the distances in undesirable ways.
The -surface-vertex-areas command does indeed output the vertex areas as they are used in our processing. Again, you should use individual surfaces when possible. If you want to see how we compute these, the most relevant starting points are here: https://github.com/Washington-University/workbench/blob/master/src/Files/SurfaceFile.cxx , search for "computeNodeAreas" https://github.com/Washington-University/workbench/blob/master/src/Files/GeodesicHelper.h Tim On Thu, Nov 20, 2014 at 4:30 PM, Benjamin Risk <[email protected]> wrote: > Hello, > > I am trying to define a neighborhood structure for vertices in the > cortical surface used in the fMRISurface pipeline. My understanding is that > the minimally preprocessed subject data are spatially matched to the 32k > Conte69 midthickness surface. I would like to use the same distance > structure that was used in the preprocessing pipeline as described in > Glasser et al (2013) p.121 paragraph two. Does a 32k x 32k matrix (or 29k x > 29k excluding medial wall) of distances between neighboring vertices > already exist (e.g., sparse matrix with distances for vertices within 3 > sigma defined using a 2mm FWHM Gaussian kernel)? If not, is the best way to > generate such a matrix by looping through the vertices and using the > wb_command -surface-vertex-areas with limit set to 3*0.8493 or similar? > > On a separate note, I am also interested in the "vertex areas" used in the > pre-processing pipeline. Does the command below reproduce these areas? > > wb_command -surface-vertex-areas Conte69.R.midthickness.32k_fs_LR.surf.gii > myfile.gii > > > Many thanks! > Ben Risk > > Graduate Student > Department of Statistical Science > Cornell University > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
