Hi Estrid, Help from others is likely to be needed, but I can help a little.
The HCP surfaces get to 32k_fs_LR mesh via the Freesurfer registration (?h.sphere.reg); however, the fs_LR mesh is not the same as the fsaverage mesh, even though it is based on it. The fsaverage left and right hemispheres are not in registration with one another. Vertex i in the left hem could be in the occipital lobe, while it could be in the frontal lobe in the right hem. The fs_LR mesh is in register across hemispheres -- vertices in left and right hems are in as close to the same place as registration could get them to be. This facilitates cross-hem analyses. There is a relevant script here: https://github.com/Washington-University/Pipelines/blob/master/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh Specifically this line i sthe one to be studied: > #Concatenate FS registration to FS --> FS_LR registration > ${CARET7DIR}/wb_command -surface-sphere-project-unproject > "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii > > "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii > > "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii > > "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii > If you're like me, it will take a few days for you to get your head around it. But I think something like this -- projecting to one standard surface and unprojecting from another -- will be the answer. It might take multiple hops to get there, but probably only until you get the magic spheres you need to make this work. I still struggle with understanding the distinction between meshes whose vertices are in correspondence, and ones that have differing numbers of vertices, but a spatially aligned with one another. Donna On Apr 18, 2016, at 8:47 AM, Estrid Jakobsen <[email protected]> wrote: > Dear experts, > > I'm trying to use wb_command -metric-resample to downsample a vector of data > points from fs_LR_32k (32492x1) to fsaverage5 (10242x1) space. > > If I'm not mistaken, this should be possible without prior registration, > because the HCP fs_LR_32k surfaces and the fsaverage5 surface should already > be in register. I've saved my data vector as a metric gifti file > (data.func.gii) in matlab by loading a pre-existing .gii file using the gifti > toolbox and replacing gifti.cdata with my own data vector. I'm then running > the following command: > > wb_command -metric-resample data.func.gii 100307.L.sphere.32k_fs_LR.surf.gii > fsa5.lh.sphere.surf.gii ADAP_BARY_AREA data_fsa5.func.gii -area-surfs > 100307.L.inflated.32k_fs_LR.surf.gii fsa5_lh.inflated.surf.gii -current-roi > mask.func.gii -valid-roi-out roi_out.func.gii > > The command runs without errors, but the output looks strange (see > attachment). It seems as though the neighborhood information is preserved but > the coordinates are not, especially obvious by the medial wall mask being > shifted anterior. I've tried running the command with and without the > -area-surfs and -current-roi (to mask out the medial wall) options, neither > of which seem to make any difference. > > Any suggestions as to what might be going wrong here would be very much > appreciated. > Thanks! > > Estrid > > **************** > Estrid Jakobsen > PhD Student, IMPRS NeuroCom > Department of Neurophysics > Max Planck Research Group Neuroanatomy and Connectivity > Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig > +49 341 9940-2423 > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > <groupconn45_fsa5.png> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
