From 3cfff7f76145747a40f51fe286fbd5006d24bcf6 Mon Sep 17 00:00:00 2001
From: Marco Barbieri <42785273+barma7@users.noreply.github.com>
Date: Tue, 23 Oct 2018 17:32:54 -0700
Subject: [PATCH] Update femoral_cartilage.py

fixed bug for split_regions method.
Center of mass was evaluated considering also the background causing severe errors for medial and lateral estimation.
---
 tissues/femoral_cartilage.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tissues/femoral_cartilage.py b/tissues/femoral_cartilage.py
index fcd0a2e..88ae14c 100644
--- a/tissues/femoral_cartilage.py
+++ b/tissues/femoral_cartilage.py
@@ -174,11 +174,12 @@ def split_regions(self, unrolled_quantitative_map):
         unrolled_mask_indexes = np.nonzero(unrolled_quantitative_map)
         unrolled_mask = np.zeros((unrolled_quantitative_map.shape[0], unrolled_quantitative_map.shape[1]))
         unrolled_mask[unrolled_mask_indexes] = 1
-        unrolled_mask[np.where(unrolled_mask < 1)] = 3
 
         # find the center of mass of the unrolled mask
         center_of_mass = sni.measurements.center_of_mass(unrolled_mask)
 
+        unrolled_mask[np.where(unrolled_mask < 1)] = 3
+
         lateral_mask = np.copy(unrolled_mask)[:, 0:np.int(np.around(center_of_mass[1]))]
         medial_mask = np.copy(unrolled_mask)[:, np.int(np.around(center_of_mass[1])):]