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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Seán Froudist Walsh <froud...@tcd.ie<mailto:froud...@tcd.ie>> Date: Wednesday, January 3, 2018 at 10:29 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 HCP-Users@humanconnectome.org<mailto: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
