Note that this command just makes the left hemisphere take precedence - you said the overlap was in medial wall, which is more of an artifact of processing than a structure of importance, so this should be fine. The surfaces shouldn't have any overlap on real structures, so ribbon constrained surface to volume mapping should prevent any other serious overlaps.
Tim On Mon, Oct 3, 2016 at 8:56 PM, Timothy Coalson <[email protected]> wrote: > Assuming that your label values don't have any overlap (each integer > uniquely identifies not only the area but also the hemisphere), you can do > the math part with wb_command -volume-math: > > wb_command -volume-math 'L + (L == 0) * R' ${Subject}.custom_raw.nii.gz > -var L ${Subject}.L.custom.nii -var R ${Subject}.R.custom.nii > > You can then make the combined label names text file and use it to > reimport the label file: > > wb_command -volume-label-export-table ${Subject}.L.custom.nii 1 > ${Subject}.L.custom.txt > wb_command -volume-label-export-table ${Subject}.R.custom.nii 1 > ${Subject}.R.custom.txt > cat ${Subject}.L.custom.txt ${Subject}.R.custom.txt > > ${Subject}.custom.txt > wb_command -volume-label-import ${Subject}.custom_raw.nii.gz ${ > Subject}.custom.txt ${Subject}.custom.nii.gz > > I also suggest using .nii.gz, label files compress very well. Unlike FSL, > workbench doesn't have an environment variable controlling the output > format, you must specify full filenames. > > Tim > > > On Mon, Oct 3, 2016 at 8:29 PM, Simon Baker <[email protected]> > wrote: > >> Hi all, >> >> We want to use our own custom parcellation with the connectome project >> data. Ultimately the parcellation needs to be a NIFTI volume. >> >> We mapped our own custom parcellation from fsaverage (.annot file in >> FreeSurfer space) onto an HCP subject (GIFTI surface .label.gii file in >> ${Subject}/MNINonLinear space) separately for each hemisphere, and we would >> like to convert the GIFTI surface files into a NIFTI volume file. Although >> this can be done with the following commands . . . >> >> [MNINonLinear]$ wb_command -label-to-volume-mapping >> ${Subject}.L.custom.164k_fs_LR.label.gii >> ${Subject}.L.sphere.164k_fs_LR.surf.gii >> T1w.nii.gz ${Subject}.L.custom.nii -ribbon-constrained >> ${Subject}.L.white.164k_fs_LR.surf.gii ${Subject}.L.pial.164k_fs_LR.s >> urf.gii >> >> [MNINonLinear]$ wb_command -label-to-volume-mapping >> ${Subject}.R.custom.164k_fs_LR.label.gii >> ${Subject}.R.sphere.164k_fs_LR.surf.gii >> T1w.nii.gz ${Subject}.R.custom.nii -ribbon-constrained >> ${Subject}.R.white.164k_fs_LR.surf.gii ${Subject}.R.pial.164k_fs_LR.s >> urf.gii >> >> [MNINonLinear]$ fslmaths ${Subject}.L.custom.nii -add >> ${Subject}.R.custom.nii ${Subject}.custom.nii >> >> . . . we have found that some voxels on the medial wall are labelled as >> both a left hemisphere region and a right hemisphere region. >> >> Using wb_command, how can we generate a NIFTI volume file containing both >> the left hemisphere parcellation and the right hemisphere parcellation and >> ensure that each voxel is labelled as only one region? >> >> Kind regards, >> >> Simon Baker >> Brain & Mental Health Laboratory >> Monash Institute of Cognitive & Clinical Neurosciences >> Monash University >> >> _______________________________________________ >> 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
