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:

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.

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 (1/2)

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	143:164	4	7.84346	0.25769	12.59003	0.19706
single_subject/data/t2/t2_seg.nii.gz	165:186	3	8.07711	0.12172	12.23168	0.215

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

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	143:164	4	0.78131	0.02058	6.45375	2.47327	0.97215	0.00925	17.95767
single_subject/data/t2/t2_seg.nii.gz	165:186	3	0.75055	0.01285	0.95162	0.65276	0.97003	0.00736	17.81215