Verify the correctness of the metrics#

You may have noticed that the csv files generated by sct_process_segmentation also include the angles between the cord centerline and the normal to the axial plane. angle_AP corresponds to the angle about the AP axis, while angle_RL corresponds to the angle about the RL axis. These angles are used to correct for the tilt of the spinal cord relative to the superior-inferior axis. Therefore, if you obtain inconsistent CSA values, it is a good habit to verify that the values of these angles are reasonable.

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

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

AP and RL angles produced in csa_perlevel.csv#

Filename

Slice (I->S)

VertLevel

MEAN(angle_AP)

STD(angle_AP)

MEAN(angle_RL)

STD(angle_RL)

single_subject/data/t2/t2_seg.nii.gz

143:164

4

0.95197

0.2383

11.40617

0.3825

single_subject/data/t2/t2_seg.nii.gz

165:186

3

1.69266

0.52528

8.58325

1.23014