Dear Marco,

This QC scores represent the expected Dice of the segmentations. Of course, computing the real Dice requires reference segmentations, but this estimate is pretty good at picking up bigger segmentation mistakes, insufficient field of view, etc.

One way to use the QC scores is to reject the cases with one or more values under a threshold, e.g., 0.7.

You can find further details in this paper:   https://www.pnas.org/doi/10.1073/pnas.2216399120

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: Marco Ganzetti <marco.ganzetti@biogen.com>
Date: Friday, June 27, 2025 at 06:09
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] QC Synthseg

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I would like to know how to interpret the QC output from the SynthSeg application. What do they mean and how they are computed?

Marco