/sagittal_lumbar_seg

This tutorial explains how to segment spinal cords on images with sagittal orientation and thick slices.

lumbar_sagittal_seg

This tutorial explains how to segment spinal cords on images with sagittal orientation and thick slices. In general we highly recommend to segment the cord on isotropic resolution data, or data acquired axially. However, in some cases, you might want to obtain a rough delineation of the cord from sagittal scans. Here's a suggestion on how to do it.

Dependencies

SCT version: v3.2.1.

Getting started

Below is an example of a sagittal scan. You notice that the spinal cord is difficult to delineate on the axial view, due to the low resolution in the right-left direction:

The strategy here is to resample the scan to an isotropic resolution, and then segment the cord using manual initialization.

# resample
sct_resample -i T2.nii.gz -mm 1x1x1 -o T2r.nii.gz
# segment with manual initialization
sct_propseg -i T2r.nii.gz -c t2 -init-centerline viewer

The image below shows how to do the manual initialization. Here, we only label until the lower tip of the spinal cord, which stops at around T12-L1. Below the spinal cord is the cauda equine.

And here is the resulting cord segmentation:

If you wish to resample the segmentation at the same resolution of the native image, you can do so using the following command:

# resample back to T2 native space
sct_register_multimodal -i T2r_seg.nii.gz -d T2.nii.gz -identity 1 -x linear

Note, here we used linear interpolation in order to keep the partial volume information, but you can also output a binary segmentation by replacing -x linear by -x nn. Here is the output:

License

The MIT License (MIT)

Copyright (c) 2018 École Polytechnique, Université de Montréal

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