Normalization pipeline#

Morphometrics measures are output from sct_process_segmentation and include cross-sectional area (area), anteroposterior diameter (diameter_AP), right-left diameter (diameter_RL), eccentricity and solidity. Metrics are normalized using the non-compressed levels above and below the compression site using the equation in the figure below.

Additionally, if the -normalize-hc 1 flag is used, metrics are normalized using a database built from adult healthy participants. This database uses the PAM50 template as an anatomical reference system.

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/sb/4158-add-tutorial-sct-compute-compression/spinalcord-compresssion-norm/normalized_metrics_hc_figure.png

Normalized metric ratio using a database of healthy controls.#

Legend:
  • mi : metric at the compression level.

  • ma : metric above the compression levels.

  • mb : metric below the compression level.