Summary of what happened:
I am trying to create a .dlabel.nii atlas out of the Desikan-Killiany parcellation done by FreeSurfer.
-
I followed the HCP guidelines on how to convert FreeSurfer label files to GIFTI format, and then used these as the left and right cortical surface label inputs into
wb_command -cifti-create-label
. -
For the subcortical volume part, I changed the FreeSurfer aparc+aseg.mgz file into Nifti using
mri_convert
and then changed it into a label volume usingwb_command -volume-label-import
.
mri_convert aparc+aseg.mgz aparc+aseg.nii
wb_command -volume-label-import aparc+aseg.nii FreeSurferAllLut.txt aparc+aseg_label.nii -drop-unused-labels
where FreeSurferAllLut.txt
is the label table with the following format (first few lines of the file):
LEFT-CEREBRAL-EXTERIOR
1 70 130 180 255
LEFT-CEREBRAL-WHITE-MATTER
2 245 245 245 255
LEFT-CEREBRAL-CORTEX
3 205 62 78 255
LEFT-LATERAL-VENTRICLE
4 120 18 134 255
However, when I run
wb_command -cifti-create-label aparc+aseg_dseg.dlabel.nii \
-left-label aparc_lh.32k_fs_LR.label.gii \
-right-label aparc_rh.32k_fs_LR.label.gii \
-volume aparc+aseg_label.nii aparc+aseg_label.nii
I get the following error:
ERROR: volume label file does not contain any structure names
What could be causing this? I guess the conversion of the parcellation into a label volume was unsuccessfull, but I have no idea what could have gone wrong.
Version:
Connectome Workbench Version: 2.0.1