I have data from 2 sessions and want to check to what extent the positioning of the participants differed, especially wrt how they tilted their head towards their chest. To get some info on this, I used the sct_processs_segmentation on the segmentations of the highres T2w data from Siemens SPACE sequence, so the orientations should be the same as in the course material.
However, I am confused about the angles - from the sct course documentation it seems as if angle_AP actually refers to the tilt in the left-right directions, and angle_RL describes the tilt in the AP plane? I am a bit confused now, especially since the angle_AP is usually larger in my data than angle_RL, and then the sct course description does not make sense to me, as they did not tilt their head strongly in the left or right direction.
Thanks a lot for your help!
Alice

Thank you for your question. For the purpose of the measure you want, it is the angle_RL you should take. It is not suprising that you get higher values than the ones in the SCT course. The angle value is dependent on what you averaged your morphometrics in sct_process_segmentation. In the course, it was averaged on C2-C3 levels. If you want to compare head tilting, you can measure angle_RL at C2 for example and at C6 and substract them to get the neck tilting angle of the participant.

Hi Sandrine,
thanks a lot for your answer. I just used a C6 mask, since I thought the angle information would tell me the tilt across the entire mask? But if I understand you correctly, it would make more sense to take the angle at the highest and lowest z in the mask, and subtract them to get the tilt in only that section?
Thanks a lot Best regards,
Alice

The angle information is only on the level you averaged your metrics on. You can use your highest and lowest levels to compute the angle and substract them to get the tilt, you got the right idea .