Other shape metrics

The csv files generated by sct_process_segmentation also include additional metrics (besides area) to analyse the shape of the spinal cord in the axial plane:

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/shape-metric-computation/sct_process_segmentation-shape-metrics.png

CSV key

Meaning

diameter_AP

Antero-posterior diameter

diameter_RL

Right-left diameter

eccentricity

Eccentricity of the ellipse that has the same second-moments as the spinal cord. Eccentricity is the ratio of the focal distance over the major axis length. The value is in the interval [0, 1). When it is 0, the ellipse becomes a circle.

solidity

CSA(spinal_cord) / CSA_convex(spinal_cord). The more ellipse-shaped the cord is (i.e. the closer the perimeter of the cord is to being fully convex), the closer the solidity ratio will be to 1. This metric is interesting for detecting concave regions (e.g., in case of strong compression).

orientation

Angle (in degrees) between the AP axis of the spinal cord and the AP axis of the image.

symmetry_dice

Dice score between the left and right (RL) hemicords or anterior and posterior (AP) halves of the spinal cord.

symmetry_hausdorff

Hausdorff distance between the left and right (RL) hemicords or anterior and posterior (AP) halves of the spinal cord.

symmetry_difference

Absolute difference between the left and right (RL) hemicords or anterior and posterior (AP) halves of the spinal cord.

area_quadrant

Cross-sectional area of the spinal cord in each quadrant (anterior-left, anterior-right, posterior-left, posterior-right).

These are of particular interest for studying cord compression. See Martin et al. BMJ Open 2018 and Horáková et al. Quant Imaging Med Surg 2022 for example applications.

For an interactive database of normative values, see Valošek, Bédard et al. NeuroLibre 2023.

To demonstrate, below are the shape metrics provided in the CSV file produced by CSA (Per level).

Additional shape metrics produced in csa_perlevel.csv (1/3)

Filename

Slice (I->S)

VertLevel

MEAN(diameter_AP)

STD(diameter_AP)

MEAN(diameter_RL)

STD(diameter_RL)

single_subject/data/t2/t2_seg.nii.gz

145:168

4

7.557797393729964

0.371714499965087

12.171986789402714

0.2349745566524634

single_subject/data/t2/t2_seg.nii.gz

169:189

3

7.799063337542908

0.2171612098434197

11.597291293370072

0.2097014530638874
Additional shape metrics produced in csa_perlevel.csv (2/3)

Filename

Slice (I->S)

VertLevel

MEAN(eccentricity)

STD(eccentricity)

MEAN(orientation)

STD(orientation)

MEAN(solidity)

STD(solidity)

SUM(length)

single_subject/data/t2/t2_seg.nii.gz

145:168

4

0.7719048859169844

0.0309394700240913

4.154214110014227

2.7906883828338245

0.9598203196975202

0.0118961728448969

19.7634319562494

single_subject/data/t2/t2_seg.nii.gz

169:189

3

0.7360108959634977

0.0146247883136632

-0.3481443435020262

1.433454047290451

0.9571264138338458

0.0116251565625195

17.032696218554673
Additional shape metrics produced in csa_perlevel.csv (3/3)

Filename

Slice (I->S)

VertLevel

MEAN(area_quadrant_anterior_left)

MEAN(area_quadrant_anterior_right)

MEAN(symmetry_dice_RL)

MEAN(symmetry_dice_AP)

MEAN(symmetry_hausdorff_RL)

MEAN(symmetry_hausdorff_AP)

single_subject/data/t2/t2_seg.nii.gz

145:168

4

18.755862248881183

18.283371245434328

0.9199521049650894

0.9188835783083904

0.6104761281195848

0.6979441337345547

single_subject/data/t2/t2_seg.nii.gz

169:189

3

17.433448483702904

18.187617393536364

0.9247183806292548

0.9226552951853212

0.5935347313120352

0.5587214936652286