How to compute CSA from brain data

The following example will show how to compute CSA on T1w scans which were acquired for the brain, but where the upper cervical spinal cord is visible:


# This code has been tested with SCT v4.2.1
# Download example data
sct_download_data -d sct_example_data
# Crop to simulate a brain-only scan with the cord visible down to C2-C3 disc
sct_crop_image -i t1.nii.gz -zmin 125
# Segment the spinal cord, specifying that a brain is present in the image
sct_deepseg_sc -i t1_crop.nii.gz -c t1 -brain 1 -centerline cnn
# Label vertebrae
sct_label_vertebrae -i t1_crop.nii.gz -s t1_crop_seg.nii.gz -c t1
# Compute average CSA between C1-C2 level
sct_process_segmentation -i t1_crop_seg.nii.gz -vertfile t1_crop_seg_labeled.nii.gz -vert 1:2

Here is the output CSA (including other morphometric measures): csa.csv (777 Bytes)