The fs_LR 32k spheres use a resolution (vertex spacing) that is suitable for 2mm fMRI data, but it sounds like you are using structural-resolution voxels. As Matt says, I would put the fs_LR surface into your volume space, and do only a single mapping, because nearest neighbor or enclosing voxel mapping is extremely lossy - additionally, I would use the 164k spheres instead.
Other forms of resampling, meant for continuous data, are not as lossy because they can approximate the underlying function, but "voxel identity" is not a continuous function. I don't know exactly what you are doing, but I would suggest mapping the data that *is* continuous onto fs_LR registered surfaces, and then re-posing your "element identity" as vertex indices, rather than T1w voxels. If this doesn't let you do what you want, then maybe you can do per-subject independent volume analysis, and then map the results of that onto the individual's surface before combining across subjects? If you want to explain your bigger-picture goal, we might have other useful suggestions. Tim On Wed, Jan 3, 2018 at 11:58 AM, Glasser, Matthew <[email protected]> wrote: > I think I would probably resample the subject’s own FS_LR registered > surfaces into the FreeSurfer space (an exact transformation) and then do a > single mapping from volume to surface. You would need to figure out the > affine matrix that describes this transform. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Seán Froudist > Walsh <[email protected]> > Date: Wednesday, January 3, 2018 at 10:29 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] volume to average surface with Nearest Neighbour > interpolation > > Dear HCP experts, > > I am interested in mapping individual voxels in a subject's FreeSurfer > conformed space (orig.nii) onto the HCP template (fsaverage_LR) while > maintaining the original voxel values. > > All of the voxels lie within the LH cortical ribbon in the (conformed) > volume space. There are 186 voxels with non-zero values that act as unique > identifiers, with all other voxels having a value of zero. > > I have prepared the native FreeSurfer to HCP transformations, then > performed volume-to-surface mapping of the sample data, and finally applied > the FreeSurfer-to-HCP transform to the sample data. I have tried to > identify the options that perform something like Nearest Neighbour > assignment, as I need to maintain the original values as identifiers. The > problem I am facing is that volume-to-surface mapping as done below reduces > the number of non-zero voxels/vertices from 186 to 94, and the > Freesufer-to-HCP resampling reduces the number of non-zero vertices further > from 94 to 13 non-zero points. > > I would greatly appreciate your guidance as to the best way to achieve my > desired goal of obtaining all 186 vertices with their original values onto > the HCP template. Should I map each voxel to the closest voxel on the > FreeSurfer WM surface, or something similar? > > The commands I used are shown below. > > Many thanks, > > Sean > > wb_shortcuts -freesurfer-resample-prep lh.white.surf.gii lh.pial.surf.gii > lh.sphere.FSave.reg.surf.gii HCP_S1200_GroupAvg_v1/standard_mesh_atlases/ > resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii > lh.midthickness.surf.gii ${current_subject}.l.midthickness.32k_fs_LR.surf.gii > lh.sphere.HCP.reg.surf.gii > > and then created a volume-to-surface mapping, while maintaining the > original voxel/vertex values using > > wb_command -volume-to-surface-mapping ' > {current_subject}_samples_LH_cortex.nii.gz > lh.midthickness.surf.gii samples_native.shape.gii -enclosing > > > > and then applied the transform using > > wb_command -metric-resample samples_native.shape.gii > lh.sphere.HCP.reg.surf.gii HCP_S1200_GroupAvg_v1/standard_mesh_atlases/ > resample_fsaverage/fs_LR-deformed_to-fsaverage.L.sphere.32k_fs_LR.surf.gii > BARYCENTRIC -largest {current_subject}_samples_HCP.shape.gii > > > _______________________________________________ > 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
