I don¹t recommend using data with large amounts of spatial smoothing (downsampling is actually a more forthright acknowledgement of what you are doing to the data and saves space and computational time). Also, it¹s worth thinking if your use case would be better served by using a brain parcellation. If correctly made, a parcellation achieves the dimensionality reduction of downsampling in a more neurobiologically informed way. If you still need to downsample the grayordiantes space, you can use an approach like this (example parameters were for creating an experimental higher resolution 1.6mm grayordinates space for 7T data):
Batch script call: GitRepo="/media/2TBB/Connectome_Project/Pipelines² #Where you have installed the HCP Pipelines code https://github.com/Washington-University/Pipelines TemplateFolder="${GitRepo}/global/templates/standard_mesh_atlases" NumberOfVertices=³59000² #set to your desired mesh vertex number OriginalMesh="164" NewMesh=³59² #what you want to call it NewResolution=³1.6² #your desired voxel resolution Caret7_Command=³wb_command² #Requires that you have installed connectome workbench SubcorticalLabelTable="${GitRepo}/global/config/FreeSurferSubcorticalLabelT ableLut.txt" ${GitRepo}/CreateNewTemplateSpace.sh ${TemplateFolder} ${NumberOfVertices} ${OriginalMesh} ${NewMesh} ${NewResolution} ${Caret7_Command} ${SubcorticalLabelTable} echo "set -- ${TemplateFolder} ${NumberOfVertices} ${OriginalMesh} ${NewMesh} ${NewResolution} ${Caret7_Command} ${SubcorticalLabelTable}" ${GitRepo}/CreateNewTemplateSpace.sh: TemplateFolder=${1} NumberOfVertices=${2} OriginalMesh=${3} NewMesh=${4} NewResolution=${5} Caret7_Command=${6} SubcorticalLabelTable=${7} ${FSLDIR}/bin/flirt -interp spline -in ${TemplateFolder}/Avgwmparc.nii.gz -ref ${TemplateFolder}/Avgwmparc.nii.gz -applyisoxfm ${NewResolution} -out ${TemplateFolder}/Atlas_ROIs.${NewResolution}.nii.gz ${FSLDIR}/bin/applywarp --rel --interp=nn -i ${TemplateFolder}/Avgwmparc.nii.gz -r ${TemplateFolder}/Atlas_ROIs.${NewResolution}.nii.gz --premat=$FSLDIR/etc/flirtsch/ident.mat -o ${TemplateFolder}/Atlas_ROIs.${NewResolution}.nii.gz ${Caret7_Command} -volume-label-import ${TemplateFolder}/Atlas_ROIs.${NewResolution}.nii.gz ${SubcorticalLabelTable} ${TemplateFolder}/Atlas_ROIs.${NewResolution}.nii.gz -discard-others -drop-unused-labels ${Caret7_Command} -surface-create-sphere ${NumberOfVertices} ${TemplateFolder}/R.sphere.${NewMesh}k_fs_LR.surf.gii ${Caret7_Command} -surface-flip-lr ${TemplateFolder}/R.sphere.${NewMesh}k_fs_LR.surf.gii ${TemplateFolder}/L.sphere.${NewMesh}k_fs_LR.surf.gii ${Caret7_Command} -set-structure ${TemplateFolder}/R.sphere.${NewMesh}k_fs_LR.surf.gii CORTEX_RIGHT ${Caret7_Command} -set-structure ${TemplateFolder}/L.sphere.${NewMesh}k_fs_LR.surf.gii CORTEX_LEFT for Hemisphere in L R ; do ${Caret7_Command} -metric-resample ${TemplateFolder}/${Hemisphere}.atlasroi.${OriginalMesh}k_fs_LR.shape.gii ${TemplateFolder}/fsaverage.${Hemisphere}_LR.spherical_std.${OriginalMesh}k _fs_LR.surf.gii ${TemplateFolder}/${Hemisphere}.sphere.${NewMesh}k_fs_LR.surf.gii BARYCENTRIC ${TemplateFolder}/${Hemisphere}.atlasroi.${NewMesh}k_fs_LR.shape.gii -largest ${Caret7_Command} -surface-cut-resample ${TemplateFolder}/colin.cerebral.${Hemisphere}.flat.${OriginalMesh}k_fs_LR. surf.gii ${TemplateFolder}/fsaverage.${Hemisphere}_LR.spherical_std.${OriginalMesh}k _fs_LR.surf.gii ${TemplateFolder}/${Hemisphere}.sphere.${NewMesh}k_fs_LR.surf.gii ${TemplateFolder}/colin.cerebral.${Hemisphere}.flat.${NewMesh}k_fs_LR.surf. gii done You can then create the template grayordinates space with wb_command -cifti-create-dense-scalar <TemplateGrayordinateSpace> -volume ${TemplateFolder}/Atlas_ROIs.${NewResolution}.nii.gz ${TemplateFolder}/Atlas_ROIs.${NewResolution}.nii.gz -left-metric ${TemplateFolder}/L.atlasroi.${NewMesh}k_fs_LR.shape.gii -roi-left ${TemplateFolder}/L.atlasroi.${NewMesh}k_fs_LR.shape.gii -right-metric ${TemplateFolder}/R.atlasroi.${NewMesh}k_fs_LR.shape.gii -roi-right ${TemplateFolder}/R.atlasroi.${NewMesh}k_fs_LR.shape.gii You can use wb_command -cifti-resample from the 2mm standard grayordiantes space to your new one (it¹s recommended that you use the individual subject¹s midthickness surfaces as area surfaces or group average vertex areas when doing the resampling so that you treat each square mm of cortex the same). If you are doing a simple resampling (no registration), you don¹t need to specify any volume transformation. CUBIC is the recommended volume resampling method and ADAP_BARY_AREA is the recommended surface resampling method for continuous data. If you need to resample midthickness surfaces to use as area surfaces, you can do that with wb_command -surface-resample (for surfaces use the BARYCENTRIC resampling method). In most cases though, rather than downsampling parcellation is a better approach. Peace, Matt. On 5/5/15, 4:15 PM, "Eric Wong" <ecw...@ucsd.edu> wrote: >Hello, >I am interested in looking at the HCP grayordinate space data, but at >various levels of reduced resolution. My understanding is that various >levels of in-plane smoothing are available through FSL, but that the >resulting smoothed data is still on the full grayordinate mesh? Are there >coarser (decimated) meshes to which one could downsample the data to >perform lower resolution surface based analyses? I could always apply >standard mesh decimation methods to the data, but if coarser meshes >already exist, we may as well use the same ones. Alternatively, if I was >to generate my own decimated meshes (which I would be happy to share), >presumably it would make the most sense to decimate the mesh using >whatever canonical surface geometry was used to define the original gray >ordinate mesh in the first place. Is this surface geometry available? >Thank You, >Eric Wong >_______________________________________________ >HCP-Users mailing list >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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
