Spinal cord segmentation for MT1 data

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

sct_deepseg_sc -i mt1.nii.gz -c t2 -qc ~/qc_singleSubj

Input arguments

• -i : Input image.

• -c : Contrast of the input image. T2 is chosen because of the visual similarity between MT and T2 contrasts.

• -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_sc