Dear Victor,
That’s a good question!
We inform the estimation of the gray matter intensities with the median of the voxels segmented as GM in the main stream. Because the median is a robust statistic, the thalamic nucleia and hippocampal subfields should be fine. But yes,
you’re definitely better off QCing.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng@bidmc.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, March 15, 2020 at 14:24
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HP and thalamic subfield quality with a bad aparc segmentation
Hi all,
From my understanding from the log files, the subfield segmentations (and in general the aparc.mgz) relies on the norm.mgz (which is based off the brainmask.mgz). What if hypothetically, you have a not so good segmentation of the cerebral cortex, but willing
to individually qc the subfields for the hippo, amyg and thal to see whether they are worth including in an analysis? I don't know if you would inherently discard a subject in a subfield analysis if it has a bad cerebral cortex segmentation (e.g ring artifacts)
since the subfield segmentation retrieves some sort of cerebral cortex measurement in its calculations
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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