Fixing a failed sct_deepseg_sc segmentation#

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 -kernel argument.

  • Change the centerline detection method using the -centerline argument.

  • Try the legacy segmentation method based on mesh propagation: (sct_propseg)

  • Check the specialized models in sct_deepseg to see if one fits your use case.

  • Manually correct the segmentation.

  • Ask for help on the SCT forum.