Compute normalized morphometrics#

The sct_compute_compression function computes a ratio of the morphometric measures at the level(s) of compression with the measures at the levels above and below all compression sites.

Adding the option -normalize-hc normalizes the morphometric measures with a database of adult healthy participants before computing the ratio.

Compute ratio between AP-diameter at level of compression vs. above/below#

We will compute the ratio of the anteroposterior diameter (AP-diameter) at the level of compression and levels above and below all compresssions. This is equivalent to the MSCC (maximum spinal cord compression) metric (Miyanji et al., 2007).

sct_compute_compression -i t2_compressed_seg.nii.gz -vertfile t2_compressed_seg_labeled.nii.gz -l t2_compressed_labels-compression.nii.gz -metric diameter_AP -normalize-hc 0 -o ap_ratio.csv

Input arguments:

-i : The input segmentation file.
-vertfile : Vertebral labeling file.
-l : Compression labels file.
-metric: Metric to compute ratio: diameter_AP (default).
-normalize-hc: Set to 1 to normalize the metrics using a database of healthy controls. Set to 0 to not normalize.
-o : The output CSV file.

Output files/folders:

ap_ratio.csv : A file containing the ratio values for each. This file is partially replicated in the table below.

Anterposterior diameter ratio with levels above and below all compressions.#
filename	compression_level	slice(I->S)	diameter_AP_ratio
t2_compressed_seg.nii.gz	3.0	159	3.3493565531077407
t2_compressed_seg.nii.gz	4.0	140	11.314949666366614
t2_compressed_seg.nii.gz	5.0	118	10.780650030491945
t2_compressed_seg.nii.gz	6.0	99	21.88085837700506

Legend:

diameter_AP_ratio: Ratio computed in the subject’s native space.
diameter_AP_ratio_PAM50: Ratio computed in the PAM50 space.
diameter_AP_ratio_PAM50_normalized: Ratio computed in the PAM50 space and normalized with adult healthy participants.

Note

The flag -metric can be used to specify the morphometric to compute the ratio.
The flag -distance can be used to select the distance (mm) in the superior-inferior direction along the cord to average healthy slices.
The flag -extent can be used to specify the extent (mm) to average metrics of healthy levels.

Compute ratio of AP-diameter normalized with healthy controls#

We will add the flag -normalize-hc to use a database of adult healthy participants to normalize the anteroposterior diameters.

sct_compute_compression -i t2_compressed_seg.nii.gz -vertfile t2_compressed_seg_labeled.nii.gz -l t2_compressed_labels-compression.nii.gz -metric diameter_AP -normalize-hc 1 -o ap_ratio_norm_PAM50.csv