Hands-on: Using sct_propseg
on T2 dataΒΆ
Run the following command to process the image:
sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
- Input arguments
-i
: Input image-c
: Contrast of the input image-qc
: Directory for Quality Control reporting. QC reports allow us to evaluate the segmentation slice-by-slice
- Output files/folders
t2_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.
