Hello, I have a spinal cord segmentation and vertebral label segmentation (i.e., each vertebrae in lower / mid back labeled with a unique class) which were produced outside of SCT. Is there a way to either generate the sct vertfile from the labeled vertebral segmentation (the automatic c2-c3 detection won’t work since c2-c3 is not even in the FOV), or to calculate the morphology metrics at each vertebral label with what I have via sct?
Hi Karl,
Is there a way to either generate the sct vertfile from the labeled vertebral segmentation (the automatic c2-c3 detection won’t work since c2-c3 is not even in the FOV)
Yup, if you have the disc labels you can do e.g.:
sct_label_vertebrae -i <IMAGE> -s <SEGMENTATION> -discfile <DISCLABELS>
or to calculate the morphology metrics at each vertebral label with what I have via sct?
Yup, using:
sct_process_segmentation -i <SEGMENTATION> -vertfile <LABELED_SEGMENTATION> -vert <MIN_VERT>:<MAX_VERT> -perlevel