Merge pull request #21 from spinalcordtoolbox/jca/19-update-cord-seg

Update `PAM50_cord.nii.gz` spinal cord segmentation

scripts/label_segmentation.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# 
+# This script labels the spinal cord segmentation using the disc labels. 
+# 
+# For more context, see: https://github.com/spinalcordtoolbox/PAM50/pull/21
+# 
+# How to run:
+#   cd where this script is located and run:
+#   python label_segmentation.py
+# 
+# Author: Julien Cohen-Adad
+
+import numpy as np
+import nibabel as nib
+
+
+# Open PAM50 spinal cord segmentation
+nii_seg = nib.load("../template/PAM50_cord.nii.gz")
+
+# Open disc labels
+nii_discs = nib.load("../template/PAM50_label_disc.nii.gz")
+data_discs = nii_discs.get_fdata()
+
+# Iterate across z-slices and assign proper vertebral level value
+data_seg_labeled = nii_seg.get_fdata()
+nx, ny, nz = data_seg_labeled.shape
+disc_value = 0
+# Note: iteration is from superior (highest slice) to inferior (slice=0)
+for iz in range(nz-1, 0, -1):
+    data_seg_labeled[..., iz] *= disc_value
+    # Check if there is a disc at this slice
+    if np.any(data_discs[..., iz]):
+        # If so, update disc_value
+        disc_value += 1
+
+# Use proper dtype
+data_seg_labeled = np.uint8(data_seg_labeled)
+# Note: here we assume that PAM50_cord is also UINT8, hence there is no need to modify the header
+
+# Save file
+nii_seg_new = nib.Nifti1Image(data_seg_labeled, nii_seg.affine)
+fname_out = "PAM50_levels_new.nii.gz"
+nib.save(nii_seg_new, fname_out)
+
+print(f"Done! 🎉 \nFile created: {fname_out}")

scripts/symmetrize_cord_segmentation.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# 
+# This script creates a symmetrical image by copying the information from the right side of the image
+# to the left side.
+# 
+# It is particularly useful when manually correcting a spinal cord segmentation, because only the right
+# part needs to be corrected, and then this script is run to correct the left part. 
+# 
+# For more context, see: https://github.com/spinalcordtoolbox/PAM50/issues/19
+# 
+# How to run:
+#   cd where this script is located and run:
+#   python symmetrize_cord_segmentation.py
+# 
+# Author: Julien Cohen-Adad
+
+import numpy as np
+import nibabel as nib
+
+
+# Open PAM50 spinal cord segmentation
+nii_seg = nib.load("../template/PAM50_cord.nii.gz")
+data_seg = nii_seg.get_fdata()
+
+# Symmetrize image by copying the right to the left
+data_seg[71:, ...] = np.flip(data_seg[:70, ...], axis=0)
+
+# Use proper dtype
+data_seg = np.uint8(data_seg)
+header_seg = nii_seg.header.copy()
+header_seg.set_data_dtype(np.uint8)
+
+# Save file
+# nii_seg_new = copy.deepcopy(nii_seg)
+nii_seg_new = nib.Nifti1Image(data_seg, nii_seg.affine, header_seg)
+fname_out = "PAM50_cord_new.nii.gz"
+nib.save(nii_seg_new, fname_out)
+
+print(f"Done! 🎉 \nFile created: {fname_out}")