Fixing a failed
Due to contrast variations in MR imaging protocols, the contrast between the spinal cord and the cerebro-spinal fluid (CSF) can differ between MR volumes. Therefore, the segmentation method may fail sometimes in presence of artifacts, low contrast, etc.
You have several options if the segmentation fails:
Change the kernel size from 2D to 3D using the
Change the centerline detection method using the
Try the legacy segmentation method based on mesh propagation: (
Check the specialized models in
sct_deepsegto see if one fits your use case.
Manually correct the segmentation.
Ask for help on the SCT forum.