Hi Tim, Thanks for your email. To clarify, when I said voxels on the medial wall, I was referring to voxels near the sagittal midline of the brain (i.e., I wasn't referring to voxels that have been labelled as medial wall). As such, these voxels have been labelled as part of a structure in the left hemisphere and also labelled as part of a structure in the right hemisphere. In which case, how do you suggest we deal with the overlap issue?
Thanks again, Simon On 4 October 2016 at 13:02, Timothy Coalson <[email protected]> wrote: > 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
