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
${Subject}.L.pial.164k_fs_LR.surf.gii
[MNINonLinear]$ 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
${Subject}.R.pial.164k_fs_LR.surf.gii
[MNINonLinear]$ 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
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