The 5th vent, non-wm-hypos, left and right vessel are not worrisome. The left and right cerebral cortex are probably just a few voxels that did not get recoded to the surface parcellation. The ento and parahippo  are probably a segmentation error (good that there are only a few of them:)

On 2/7/2025 7:17 AM, tomjandrews@sky.com wrote:

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Hello,

I have run recon-all on ~1600 participants and will use the aparc+aseg.mgz parcellation to extract structural connectomes. Across the dataset, the number of labels in each parcellations ranges from 109 to 115. Where can I find a complete list of labels in aparc+aseg.mgz? The distribution of missing labels is as follows:

Label Region Name Missing Count 72    5th-Ventricle     1552 80    non-WM-hypointensities  1490 3     Left-Cerebral-Cortex    970 42    Right-Cerebral-Cortex   642 30    Left-vessel 66 62    Right-vessel      54 1006  ctx-lh-entorhinal 2 1016  ctx-lh-parahippocampal  2 2016  ctx-rh-parahippocampal  1

Among these, which missing labels are problematic? I assume the absence of the 5th ventricle and non-WM-hypointensities is expected, but I am uncertain about the others. I am only interested in the regions defined in the linked grey matter parcellations(https://github.com/MRtrix3/mrtrix3/blob/master/share/mrtrix3/labelconvert/fs...) and will restrict my structural connectome extraction to those labels. However, do these missing labels above suggest segmentation issues?

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Best, Tom

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