Subcortical

1. What you rate

• The FreeSurfer subcortical segmentation: the colored labels covering the deep brain structures.
• Look at all the structures together. They are located close together, so one look usually covers all of them.
  • Everything looks fine? PASS all structures and move on.
  • Something looks wrong? Figure out which structure(s) are affected, and fail only those. Rate left and right separately (the brainstem is a single region).

Which regions?

Group	Structure	Color	Best view
Basal ganglia	Caudate	Light blue-gray	Anterior coronal, superior horizontal, lateral sagittal
	Putamen	Pink	Coronal, inferior horizontal
	Pallidum	Blue	Posterior coronal, inferior horizontal
	Accumbens area	Orange	Anterior coronal
Diencephalon	Thalamus	Green	Posterior coronal, inferior horizontal
	Ventral Diencephalon	Salmon	Posterior coronal, medial sagittal
Limbic	Hippocampus	Yellow	Posterior coronal, lateral sagittal
	Amygdala	Cyan	Posterior coronal, lateral sagittal
Brainstem	Brainstem	Light blue-gray (distinguish from caudate by location)	Medial sagittal
Cerebellum	Cerebellum white matter	Light yellow-green	Medial and lateral sagittal
	Cerebellum cortex	Brown	Medial and lateral sagittal

Not rated: inferior lateral ventricle (purple) and choroid plexus (teal).

2. What you see in QC-Studio

Every participant is shown at the same slice positions. Because brains differ in size and shape, a slice doesn't always land in the same spot in the brain, so a structure may be hard to see in one view. If so, use the other views.

3. What to check and how to rate

Problem	Question to ask	What it looks like	Still PASS	FAIL
Distorted or misplaced structure	Does each structure have roughly the right shape and position?	A label has a very strange shape or sits in the wrong place.	Minor shape differences or asymmetry between left and right	Very distorted or clearly misplaced
Overestimation	Does each label stay within its structure?	A label extends into surrounding tissue, for example the caudate spreading over the white matter above the ventricle.	Slight extension at the edge	The label clearly extends along a large stretch of the neighboring tissue
Missing part	Is the whole structure labeled?	Part of a structure has no label, often the cerebellum after a failed skull strip.	Small bits missing	A large part is missing
Widespread failure	Do the labels look reasonable overall?	Many or all structures look wrong at the same time, often after motion or a failed skull strip.	—	Fail each affected structure

• Errors are rare in the subcortex. Most structures should pass.
• Problems are often widespread. If one structure fails, check its neighbors.

4. Examples

Good segmentation

Rows from top to bottom: sagittal, coronal, and horizontal views.

Common problems

Problem	What happens	Rating	Example
All structures failed	The segmentation failed for all subcortical structures except the cerebellum	FAIL all affected structures
Caudate overestimated	The caudate label spreads over the white matter above the lateral ventricle	PASS if slight. FAIL if it extends along most of the ventricle
Failed skull strip	The bottom of the cerebellum is cut off by the brain mask, so it's not labeled	FAIL cerebellum white matter and cerebellum cortex

Other situations

Situation	What to do
White matter hypointensities (light purple, often around the ventricles)	Not an error. These are white matter spots that look dark on T1
A structure is hard to see in a view because of the slice position	Use the other views to judge it
A problem in one hemisphere only	Fail only that side
Part of the cerebellum is cut off in the T1 scan	FAIL cerebellum white matter and cortex on the affected side
The T1 quality was poor, but the labels look correct	PASS. Rate the segmentation, not the scan
The head was tilted in the scanner, so left and right structures appear at different heights or sizes in the same slice	PASS if each label fits its structure. Check the other views to confirm