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, tomjandr...@sky.com wrote:
External Email - Use Caution
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_default.txt)
and will restrict my structural connectome extraction to those labels.
However, do these missing labels above suggest segmentation issues?
Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96
uname -a: Linux login-d 4.18.0-348.20.1.el8_5.x86_64 #1 SMP Tue Mar 8
12:56:54 EST 2022 x86_64 x86_64 x86_64 GNU/Linux
Best,
Tom
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
