Template/Atlas-based lesion analysis

The sct_analyze_lesion function allows you to provide a folder containing an atlas/template registered to an anatomical image. If specified, the function computes:

  1. for each lesion, the proportion of that lesion within each vertebral level and each region of the template (e.g. GM, WM, WM tracts). Each cell in the output XLS file contains a percentage value representing how much of the lesion volume exists within the region indicated by the row/column (rows represent vertebral levels, columns represent ROIs). The percentage values are summed to totals in both the bottom row and the right column, and the sum of all cells is 100 (i.e. 100 percent of the lesion), found in the bottom-right.

  2. the proportions of each ROI (e.g. vertebral level, GM, WM) occupied by lesions.

Note

The following command requires that you register the PAM50 template to the t2.nii.gz anatomical image. You can register the template and warp the atlas to the anatomical image using the sct_register_to_template and sct_warp_template functions, respectively. Specifically, the following command is vital to run before using -f label, since it generates the label/ folder in the working directory.

If you have downloaded the .zip containing the prerequisite files, then you will have access to a pre-computed warping field based on the sample image:

# Generate the subject-space label/atlas folder required by `-f label`
sct_warp_template -d t2.nii.gz -w ../t2/warp_template2anat.nii.gz

See template-registration for more information on the steps used to generate this file.

Running sct_analyze_lesion

sct_analyze_lesion can be applied to lesion and spinal cord segmentation masks using the following command

sct_analyze_lesion -m t2_lesion_seg.nii.gz -s t2_sc_seg.nii.gz -f label -qc ~/qc_singleSubj
Input arguments:

  • -m : 3D binary mask of the segmented lesion

  • -s : 3D binary mask of the segmented spinal cord

  • -f : Folder containing the atlas/template registered to the anatomical image

  • -qc : Directory for Quality Control reporting. QC report contains a figure for the tissue bridges