On Mon, Jul 24, 2017 at 8:40 AM, Claude Bajada <c.baj...@fz-juelich.de> wrote:
> Dear all, > > I have a two questions about the surfaces that live in the HCP data > folders: > > 1. MNINonLinear/fsaverage/ > 2. T1w/fsaverageLR32k/ > > I assume you mean the fsaverage_LR32k folder within each of those folders. > If I have understood the minimal pipeline correctly: > > 1. all the surfaces in MNINonLinear/fsaverage32k/ are the individual's > surface that was warped into a template space (either FS or MSMAll). > 2. the surfaces in T1w/fsaverageLR32k/ are the surfaces mentioned in > the above point that are warped back into the individual's native space > > Not exactly. Volume spaces are a completely orthogonal question to surface registration. Except for some special files, everything in the MNINonLinear folder aligns to the MNI template via FNIRT registration. Everything in T1w similarly aligns to the subject's AC-PC rigid aligned space (original size and shape of the subject's structural scans, just rotated and moved to the usual orientation). MSMAll, freesurfer, MSMSulc, or any other surface registration does not cause any anatomical deformations of the individual's brain. The standard mesh anatomical surfaces you get after surface registration and resampling align with the same volumes as the original surfaces. There is no pre-defined anatomical coordinate template in our surface atlases, so we don't need to work backward from any template coordinate system. Instead, we have standard spheres that define the standard topology (triangle relationships) - once we have the subject's sphere aligned to the standard sphere via template data (sulc for MSMSulc or FS; resting state networks, myelin, thickness, etc for MSMAll), we can combine the standard sphere's topology with the subject's anatomical coordinate data (by resampling the XYZ values), generating the subject's standard mesh surfaces. The surfaces in T1w are generated first, as we run freesurfer on the structural scans to generate them. We then apply the FNIRT warpfield to them to get the MNINonLinear versions. As a side note, group average surfaces ARE significantly deformed from the individuals' brain shapes. Most notably, they contain much less folding, and therefore surface area, as all the incompatible or non-corresponding folding patterns (when you align based on function, folding becomes less aligned, as function isn't always fixed with respect to folds) effectively smooth each other out when averaged. This is why we have correction methods for this when doing spatial operations on group average surfaces. > The two questions are: > > 1. Given the above, am I right in assuming that any data that > correspond to a vertex of a surface in T1w/fsaverageLR32k/ also corresponds > to the surface in MNINonLinear/fsaverageLR32k/? > > Yes. > 2. Do you recommend that we the MSMAll surfaces over the FS ones? Yes, they have considerably better cross subject functional correspondence than freesurfer. That is, if a given vertex index is in area MT in one subject, MSMAll will have a considerably higher percentage of other subjects that also have that vertex in MT. > Regards, > > Claude > > > > > ------------------------------------------------------------ > ------------------------------------ > ------------------------------------------------------------ > ------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > ------------------------------------------------------------ > ------------------------------------ > ------------------------------------------------------------ > ------------------------------------ > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
