License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 19, 2022
Last Modified: November 30, 2022
Protocol Integer ID: 70208
Abstract
This protocol is a guide to conducting a visual quality control (QC) of Freesurfer outputs. Quality control is important to make sure that the cortical surface reconstruction and grey and white matter classification are accurate.
To examine outputs, ten images per subject are generated (see https://github.com/sbedford0/Generate_FSQC_images), showing the cortical segmentation and surface boundaries at different slices and views of the brain (3 axial; 3 coronal; 4 sagittal). The pial surface is delineated in red, and the white matter surface in blue. These images should be examined to check that the reconstructed surfaces follow the cortical boundaries accurately.
Guidelines
Rating criteria:
BAD
Missing large area, or multiple small/medium areas, of cortex
Large errors in grey/white matter boundary
MINOR ERROR
Missing small area of cortex
Minor over or under segmentation
Misclassification of GM/WM in one or two regions
GOOD
Accurate delineation of cortical boundary across the brain
Note: If Freesurfer surface looks ok or has minor errors, but scan quality is poor, rate as MOTION. If there is visible motion in the scan and Freesurfer has also performed badly (large or significant errors), rate as BAD
Materials
Example participants : good output
Example participant 1:
Example participant 2:
Example participant 3:
Examples of “issues” that are actually ok:
No Freesurfer output or cortex visible (should still be rated as “good”, as long as it doesn’t look like there is cortex that should have been included)
Large sulci or spaces that can look like holes in the reconstruction, but are actually accurately following the cortical surface (should be rated as “good” as long as you can’t see cortex and/or white matter in those spaces that was clearly missed)
Neck or shoulders included in field of view (should be rated as “good” as long as the surface reconstruction looks good - ie. ignore the extra tissue and just rate the brain as usual)
Examples of issues/bad outputs
Minor error: common issues
Missing grey matter in frontal cortex
Overestimation of cortex into skull
Slight temporal pole underestimation
Bad:
Large chunks of cortex missing
Larger sections bleeding into skull in multiple places
Temporal pole underestimation (more extensive)
More examples of temporal pole :
Note: these subjects also have visible motion in their scans. However, the Freesurfer reconstruction has large errors, so we would rate this as “bad”, to signify that it is unusable.
Motion:
Look out for: ringing or rippling effect in scans; blurry or fuzzy images
In the example below, see the blurriness of the cortex and white matter, and ringing artefact in the cerebellum:
Motion in scan (and temporal pole underestimation)
This subject has only slight underestimation of the temporal pole (only visible in sagittal view) which would usually be rated as “minor error”. However, here, the motion is more of an issue; therefore this scan would be rated as “motion”.