Computing the white matter segmentation

In the previous step, we used sct_deepseg_gm to segment the gray matter. However, to get the white matter, we essentially need the “inverse” volume. (In other words, the full spinal cord segmentation minus the gray matter segmentation.)

Segmenting the full spinal cord

In order to subtract the gray matter, we will first need to get the full spinal cord segmentation.

sct_deepseg spinalcord -i t2s.nii.gz -qc ~/qc_singleSubj

Input arguments:

• spinalcord: Task to perform. Here, we are using spinalcord to segment the spinal cord. This task is contrast-agnostic, meaning it can be used on any type of image (T1, T2, T2*, etc.)

• -i : Input image.

• -qc : Directory for Quality Control reporting. QC reports allow us to evaluate the results slice-by-slice.

Output files/folders:

• t2s_seg.nii.gz : 3D binary mask of the segmented spinal cord

Subtracting the gray matter

Now that we have the spinal cord segmentation, we can subtract the gray matter and be left with the white matter.

sct_maths -i t2s_seg.nii.gz -sub t2s_gmseg.nii.gz -thr 0 -o t2s_wmseg.nii.gz

Input arguments:

• -i : Input image. (The full segmentation of the spinal cord.)

• -sub : Flag to invoke the “subtract” functionality of sct_maths, subtracting t2s_gmseg.nii.gz from the input image.

• -thr 0: Threshold the output image to remove any negative values. (This would occur if there are voxels in the gray matter segmentation that are not in the spinal cord segmentation.)

• -o : The filename of the output image.

Output files/folders:

• t2s_wmseg.nii.gz : An image file containing the segmentation for the white matter.