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.

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	169:189	3	0.8968661357666219	0.25393920907189405	7.718045204190882	1.5169800510814218
single_subject/data/t2/t2_seg.nii.gz	190:207	2	-0.24132060791680157	0.3945752580337589	4.5851653281009055	0.2445477449142163