Extracting mean cortical thickness for each ROI defined by the HCP-MMP atlas for dHCP neonate data
Lin Cai
Dear HCP-experts,
I would like to extract the mean cortical thickness for each ROI defined by the HCP-MMP atlas from preprocessed dHCP neonatal data.
The downloaded preprocessed structural data are provided only in the native structural space. My plan is to first transform the data from native space to the dhcpSym40 surface space
(https://brain-development.org/brain-atlases/atlases-from-the-dhcp-project/cortical-surface-template/).
However, the dhcpSym cortical surface template does not include HCP-MMP atlas files.
Therefore, I decided to use the 40-week template from the UNC Spatiotemporal Neonatal Cortical Surface Atlases
(https://infantsurfatlas.projects.nitrc.org/UNC-Neonate-cortical-surface-atlas_Manual_V1.0.pdf), as this atlas provides surface files with HCP-MMP parcellation information.
Below is the analysis pipeline I am planning to use. For simplicity, it currently considers only the left hemisphere. I have tested the code, and the output files look fine.
Could you please let me know whether the overall analysis logic is reasonable, and whether there are any potential issues or improvements I should consider?
Thank you very much in advance for your help.
wb_command -metric-resample \
/rel3_dhcp_anat_pipeline/sub-CC00536XX17/ses-156900/anat/sub-CC00536XX17_ses-156900_hemi-left_desc-corr_thickness.shape.gii \
/rel3_dhcp_anat_pipeline/sub-CC00536XX17/ses-156900/xfm/sub-CC00536XX17_ses-156900_hemi-left_from-native_to-dhcpSym40_dens-32k_mode-sphere.surf.gii \
/Users/lincai/Downloads/dhcpSym_template/week-40_hemi-left_space-dhcpSym_dens-32k_sphere.surf.gii \
ADAP_BARY_AREA \
-area-surfs \
/rel3_dhcp_anat_pipeline/sub-CC00536XX17/ses-156900/anat/sub-CC00536XX17_ses-156900_hemi-left_midthickness.surf.gii \
/Users/lincai/Downloads/dhcpSym_template/week-40_hemi-left_space-dhcpSym_dens-32k_midthickness.surf.gii \
/output/sub-CC00536XX17_ses-156900_hemi-left_space-dhcpSym40_dens-32k_desc-corr_thickness.shape.gii
# From UNC 40-week label file (HCP-MMP atlas,164K) to dhcpSym 40-week label file (HCP-MMP atlas,32K) for left hemisphere
wb_command -label-resample \
/Users/lincai/Downloads/UNC/HCPFormat/40/L.ParcellationMMP.164k.label.gii \
/Users/lincai/Downloads/UNC/HCPFormat/40/L.sphere.164k.surf.gii \
/Users/lincai/Downloads/dhcpSym_template/week-40_hemi-left_space-dhcpSym_dens-32k_sphere.surf.gii \
ADAP_BARY_AREA \
-area-surfs \
/Users/lincai/Downloads/UNC/HCPFormat/40/L.white.164k.surf.gii \
/Users/lincai/Downloads/dhcpSym_template/week-40_hemi-left_space-dhcpSym_dens-32k_wm.surf.gii \
/output/sub-UNC40_to_dhcpSym40_L_MMP.32k.label.gii
# Only extract one ROI
wb_command -gifti-label-to-roi \
/output/sub-UNC40_to_dhcpSym40_L_MMP.32k.label.gii \
/output/L_V1_ROI.32k.shape.gii \
-key 1
# Calculate mean thickness for that one ROI
wb_command -metric-stats \
/output/sub-CC00536XX17_ses-156900_hemi-left_space-dhcpSym40_dens-32k_desc-corr_thickness.shape.gii \
-reduce MEAN \
-roi \
/output/L_V1_ROI.32k.shape.gii
Glasser, Matthew
For area surfs we would always use a midthickness. For group to group resampling, we would use group average vertex areas (of individual surface vertex areas) rather than a group average surface. One thing that is not at all clear is whether these data are on the fs_LR meshes or not. If they are, you could simply use the original parcellation files on the 32k_fs_LR mesh and avoid the second step (e.g., from here: https://balsa.wustl.edu/file/87B9N). If you made a CIFTI file from your thickness maps on the 32k mesh, you could simply use wb_command -cifti-parcellate to get all of the values.
Matt.
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Lin Cai
Hi Matt,
Although the authors state that the neonatal templates were generated following an initial rigid (rotational) alignment of all neonatal data to the HCP–YA fs_LR 32k template space, I do not think that the resulting neonatal surface templates are actually in the adult fs_LR 32k space. Given this, do you think it is still appropriate to use the files you provided to calculate cortical thickness maps?
Lin
Glasser, Matthew
Probably not. I would ask them how to do what you want.
Matt.