Wb_command -cifti-create-label not working with FreeSurfer aparc+aseg

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Summary of what happened:

I am trying to create a .dlabel.nii atlas out of the Desikan-Killiany parcellation done by FreeSurfer.

  1. 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.

  2. 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 using wb_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

2

For anyone struggling with the same problem, the steps which worked for me in the end were these:

  1. First register the original aparc+aseg.mgz file to the MNI space using

export SUBJECTS_DIR=%path to your FreeSurfer subject directory%

mri_cvs_register --mov %subject ID% --mni

  1. Then convert the result to Nifti

mri_convert %path to your FreeSurfer results for this subject%/cvs/final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz aparcaseg.nii.gz

  1. Then change the segmentation to a label volume

wb_command -volume-label-import aparcaseg.nii.gz FreeSurferAllLut.txt aparcaseg_label.nii.gz -drop-unused-labels

You can find the FreeSurferAllLut.txt file in the ciftify github repo (https://github.com/edickie/ciftify/blob/ce1876b22747ef76b797de5056ec38cab8fc5e66/ciftify/data/hcp_config/FreeSurferAllLut.txt#L4)

  1. Resample the atlas to the 2mm space

wb_command -volume-resample aparcaseg_label.nii.gz MNI152_T1_2mm.nii.gz ENCLOSING_VOXEL aparcaseg_dseg.nii.gz

The MNI152_T1_2mm.nii.gz template can be found in the HCPPipelines/global/templates github repo (HCPpipelines/global/templates at master · Washington-University/HCPpipelines · GitHub)

  1. When combining with cortical labels, use the -label-collision flag to avoid label clashes

wb_command -cifti-create-dense-from-template 91282_Greyordinates.dscalar.nii atlas-DesikanKilliany_space-fsLR_den-32k_dseg.dlabel.nii -volume-all aparcaseg_dseg.nii.gz -cifti aparc.32k_fs_LR.dlabel.nii -label-collision SURFACES_FIRST

The 91282_Greyordinates.dscalar.nii template can also be found in the HCPPipelines template github repo.

The whole pipeline I ended up using for this can be found here GitHub - daviddaubner42/bids_to_fc