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_default.txt) 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