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.
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 |