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parcel_naming.py

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+import nibabel as nb
+import numpy as np
+from collections import defaultdict
+
+
+# The following code was adapted from Satra Gosh's sad_figures.py script
+# located at https://github.com/satra/sad/blob/master/sad_figures.py
+
+# get cluster coordinates caculate the volume and the center of mass
+# of the brain regions in img
+
+def get_coords(img, affine):
+    coords = defaultdict(dict)
+
+    # determine the unique regions
+    labels = np.setdiff1d(np.unique(img.ravel()), [0])
+
+    for label in labels:
+
+        # calculate the volume of the region
+        coords[label]["Vol"]=np.sum(img==label)
+
+        # calculate the center of mass (CoM) of the region
+        coords[label]["CoM"]=np.dot(affine,\
+            np.hstack((np.mean(np.asarray(np.nonzero(img==label)),\
+            axis = 1),1)))[:3].tolist()
+
+    return (coords)
+