Spinal cord segmentation for MT1 data

First, we will run the sct_deepseg command to segment the spinal cord from the MT1 image (i.e. the image that has the RF off-resonance pulse applied).

sct_deepseg -task seg_sc_contrast_agnostic -i mt1.nii.gz -qc ~/qc_singleSubj

Input arguments:

• -task: Task to perform. Here, we are using seg_sc_contrast_agnostic 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:

• mt1_seg.nii.gz : 3D binary mask of the segmented spinal cord

Once the command has finished, at the bottom of your terminal there will be instructions for inspecting the results using Quality Control (QC) reports. Optionally, If you have FSLeyes installed, a fsleyes command will printed as well.

Input/output images for sct_deepseg