I’m running sct_process_segmentation on my ex-vivo rat spinal cord scans that look like this:
Looking at the images, diameter_RL should be roughly twice as long than diameter_AP on average.
The segmentation with sct_propseg looks fine it covers the whole spinal cord.
However for some reason in about 50% of the scans, in the csa.csv file the diameter values are mixed up, i.e. the diameter_AP column consists of all the values that are roughly twice of diameter_RL.
Is there something wrong with the orientation of those scans? I had to manually fix the labels to get AP and RL correct and it worked like this with the other sct functions.