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

diameter_AP_ratio_PAM50

diameter_AP_ratio_PAM50_normalized

t2_compressed_seg.nii.gz

6.0

99

26.90794564803013

t2_compressed_seg.nii.gz

4.0

140

16.89313317804684

t2_compressed_seg.nii.gz

5.0

118

10.61044087004197

t2_compressed_seg.nii.gz

3.0

159

6.391726166113154
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
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_norm_PAM50.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 normalized with healthy controls.

filename

compression_level

slice(I->S)

diameter_AP_ratio

diameter_AP_ratio_PAM50

diameter_AP_ratio_PAM50_normalized

t2_compressed_seg.nii.gz

6.0

99

26.90794564803013

27.97256039270708

26.76034036561231

t2_compressed_seg.nii.gz

4.0

140

16.89313317804684

17.954133372576663

23.878986696249484

t2_compressed_seg.nii.gz

5.0

118

10.61044087004197

11.634832516198411

16.446479733340336

t2_compressed_seg.nii.gz

3.0

159

6.391726166113154

7.771775507071121

14.577639640154317
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 -sex can be used to select the sex of adult healthy participants to use for the normalization.

  • The flag -age can be used to select the age range of adult healthy participants to use for normalization.

Compute adapted Spinal Cord Occupation Ratio (aSCOR)

You can also quantify spinal canal occupancy by first segmenting the canal, then computing aSCOR.

sct_deepseg sc_canal_t2 -i t2_compressed.nii.gz -o t2_compressed_canal_seg.nii.gz -qc ~/qc_singleSubj
sct_compute_ascor -i-SC t2_compressed_seg.nii.gz -i-canal t2_compressed_canal_seg.nii.gz -perlevel 1 -o ascor.csv
Input arguments:

  • -i-SC : Spinal cord segmentation input for sct_compute_ascor.

  • -i-canal : Spinal canal segmentation input for sct_compute_ascor.

  • -perlevel : Set to 1 to report per-level values.

  • -o : Output CSV filename.

Output files/folders:

  • ascor.csv : aSCOR values for the selected region/levels.