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.

CSA values across slices 30 to 35

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