If you compute areas on subject's native mesh, then generally correction is not necessary. But if you compute areas on a mean midthickness surface, for example (e.g., computing supratheshold area on group-derived clusters/parcels), then correction is appropriate.
The smoothing to which Tim refers is when you have a bunch of midthickness surfaces, for example, and you average them to create a mean midthickness. The areas of high variability get smoothed out, so they are not as deep/folded as the individual was, hence distances are shorter on the mean surface. Averaging occurs on the atlas mesh -- not native mesh. And Tim is advising you NOT to compute areas/distances on the mean midthickness, if you can figure out a way to do it on the individuals. This might entail bringing some group-derived ROI (e.g., label.gii) to your individual's atlas midthickness (e.g., 164k or 32k mesh surf.gii). The dtseries.nii files do not contain geometry information. They link to surf.gii files through the mesh they share. You should pair the individual's dtseries.nii with the corresponding midthickness surf.gii. Leave the Conte69 geometry out of it, for purposes like these (unless you have only group dtseries.nii, in which case you need a mean midthickness with vertex-areas). The distances between the same vertex pairs differ quite a bit across subjects. Regarding the vertex areas, could you provide a link to the pipeline source in github where this is invoked in the pipeline? Few people are familiar with this enough to know, but others might be able to shed some light if we see how it is called. I've only seen this feature used when dealing with group data, but I'm sure there are usages of which I am unaware. On Nov 21, 2014, at 8:59 AM, Benjamin Risk <[email protected]> wrote: > Great, thank you for the information! To clarify, does the smoothing and area > correction occur on the native mesh or Conte69? Do the cortical data in a > task file .dtseries.nii correspond to Conte69 midthickness, i.e., the > distances between and areas of the vertices are the same for all subjects? > > Thanks again! > Ben > > On Thu, Nov 20, 2014 at 6:12 PM, Timothy Coalson <[email protected]> wrote: > 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
