Other shape metrics

The csv files generated by sct_process_segmentation also include metrics to analyse the shape of the spinal cord in the axial plane, such as ellipticity, antero-posterior and right-left dimensions. These are of particular interest for studying cord compression. See Martin et al. BMJ Open 2018 for an example application in degenerative cervical myelopathy.

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

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