CSA (Per axial slice)¶
Finally, to compute CSA for individual slices, set the -perslice
argument to 1, and use -z
argument to specify axial slice numbers or a range of slices. (For slice numbering, 0 represents the slice furthest towards the inferior direction.)
sct_process_segmentation -i t2_seg.nii.gz -z 30:35 -perslice 1 -o csa_perslice.csv
- Input arguments
-i
: The input segmentation file.-perslice
: Set this option to 1 to turn on per-slice computation.-z
: The Z-axis slices to compute metrics for. Slices can be specified individually (30,31,32,33,34,35
) or as a range (30:35
).-o
: The output CSV file.
- Output files/folders
csa_perslice.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 |
30 |
43.0447350807718 |
0 |
|
single_subject/data/t2/t2_seg.nii.gz |
31 |
43.0291057456016 |
0 |
|
single_subject/data/t2/t2_seg.nii.gz |
32 |
41.785705898265 |
0 |
|
single_subject/data/t2/t2_seg.nii.gz |
33 |
42.3872181377957 |
0 |
|
single_subject/data/t2/t2_seg.nii.gz |
34 |
43.036500716301 |
0 |
|
single_subject/data/t2/t2_seg.nii.gz |
35 |
43.7560940584275 |
0 |