CSA (Per level)

Next, we will compute CSA for each individual vertebral level (rather than averaging).

sct_process_segmentation -i t2_seg.nii.gz -vert 3:4 -vertfile ./label/template/PAM50_levels.nii.gz -perlevel 1 -o csa_perlevel.csv
Input arguments

  • -i : The input segmentation file.

  • -vert : The vertebral levels to compute metrics across. Vertebral levels can be specified individually (3,4) or as a range (3:4).

  • -vertfile : The label file that specifies vertebral levels. Here, we use the PAM50 template object that had been previosuly warped to the same coordinate space as the T2 segmentation.

  • -perlevel : Set this option to 1 to turn on per-level computation.

  • -o : The output CSV file.

Output files/folders

  • csa_perlevel.csv : A file containing the CSA values and other shape metrics. This file is partially replicated in the table below.

CSA values computed for C3 and C4 vertebral levels

Filename

Slice (I->S)

VertLevel

MEAN(area)

STD(area)

single_subject/data/t2/t2_seg.nii.gz

143:164

4

78.0055017936352

2.53796742015513

single_subject/data/t2/t2_seg.nii.gz

165:186

3

77.7008594523071

1.56966143373016