That’s right. Matt.
From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of CHAUMON Maximilien <maximilien.chau...@icm-institute.org<mailto:maximilien.chau...@icm-institute.org>> Date: Friday, February 22, 2019 at 5:03 AM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] unwarping 164k surface to subject-specific ACPC-aligned headcoordinate space Many thanks. For reference, the command that does what I want is (note the emphasized **correction** below compared to previous). wb_command -surface-resample \ $suj/**T1w**/Native/$suj.$hemi.midthickness.native.surf.gii \ $suj/MNINonLinear/Native/$suj.$hemi.sphere.MSMAll.native.surf.gii \ $suj/MNINonLinear/$suj.$hemi.sphere.164k_fs_LR.surf.gii \ BARYCENTRIC \ $suj/T1w/$suj.$hemi.midthickness.164k_fs_LR.surf.gii Le jeu. 21 févr. 2019 à 20:29, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> a écrit : I see, I didn't realize we generated the 32k versions in T1w space but not the 164k. The output of the command should be named with "midthickness", not "sphere", the shape will be the same as the input surface. You will need to use the midthickness surface from the T1w/Native folder as the input to get the result you want (only rigidly aligned). I think the "100307.L.sphere.164k_fs_LR.surf.gii" sphere is just a copy of the standard sphere, so it should work correctly, but I'm not sure. Tim On Thu, Feb 21, 2019 at 11:00 AM CHAUMON Maximilien <maximilien.chau...@icm-institute.org<mailto:maximilien.chau...@icm-institute.org>> wrote: Thank you! In the data I have downloaded, the only place where I find a 164k surface is in the MNInonlinear directory, so I assume some nonlinear transformation has been applied. The T1w directory has no such high res surf. So This command should do what I want, right (I split in several lines for clarity) ? wb_command -surface-resample \ 100307/MNINonLinear/Native/100307.L.midthickness.native.surf.gii \ 100307/MNINonLinear/Native/100307.L.sphere.MSMAll.native.surf.gii \ 100307/MNINonLinear/100307.L.sphere.164k_fs_LR.surf.gii \ BARYCENTRIC \ 100307/T1w/100307.L.sphere.164k_fs_LR.surf.gii Many thanks for your help! Le mer. 20 févr. 2019 à 20:34, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> a écrit : Sorry, the recommended sphere for resampling any subject will of course be that subject's version of that file, not specifically subject 100307's sphere. Tim On Wed, Feb 20, 2019 at 1:31 PM Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: On Wed, Feb 20, 2019 at 8:03 AM CHAUMON Maximilien <maximilien.chau...@icm-institute.org<mailto:maximilien.chau...@icm-institute.org>> wrote: Hello, I'm looking at fine changes in MEG forward leadfields and would like to use the 164k meshes in each subject (I know 164k vertices are overkill, but I need this high res rendering for one of my figures). I'm interested in the actual original location of individual vertices in the brain in subject-specific ACPC-aligned headcoordinate space. I don't want any non linear spatial transformation applied to the mesh. So I would like to use the 164k mesh with coordinates without the nonlinear transformation that (as far as I understand) was applied to all the 164k_fs_LR files. Is there an easy way to revert the non linear transformation? Only the surface files under the MNINonLinear folder have had any nonlinear anatomical warp applied. The surface files under T1w all line up with the distortion corrected, rigidly aligned T1w image (we don't really keep scanner space around, and we often call this distortion corrected rigid alignment space "native volume space"). Surface registration/resampling does not deform the anatomy, it just tiles the same contour in 3D space with a new set of triangles. Note that averaging the coordinates of vertices across subjects will change their location, and this will affect geometry and "foldedness", to a degree depending on what registration was used. As long as you stick with individual surfaces, you don't need to worry about this. I would then use the file {Subject}.{Hemi}.midthickness.164k_fs_LR.surf.gii and apply the inverse transformation, Alternatively, is there a way to easily downsample {Subject}.{Hemi}.midthickness.native.surf.gii to 164k vertices? is this then in subject-specific ACPC-aligned headcoordinate space? how could I move to that space? This is what the existing 164k surfaces in the T1w folder already are. Native mesh is commonly ~130k for HCP scans, so 164k is actually a small upsampling. We recommend the MSMAll versions, as the same vertex number across subjects is more often in the same area than for other registrations. For reference (since we have already dealt with this resampling for you), the recommended sphere to use for resampling from native mesh to any fs_LR mesh is "MNINonLinear/Native/100307.L.sphere.MSMAll.native.surf.gii" (and the R version, of course). Ignore the fact that it is in the MNINonLinear folder, sphere surfaces don't have a volume space, that is just where it got put. The standard spheres for fs_LR are in the pipelines under global/templates/standard_mesh_atlases/, read the readme file. The command to do surface resampling is wb_command -surface-resample. Does that make sense? Many thanks, Max _______________________________________________ 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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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