correct brain extraction to get better masks

Medical-Image-Analysis-Laboratory · Oct 9, 2020 · 05ad4b6 · 05ad4b6
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commit 05ad4b6
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/...200902-170910-hkebiri-Multiple_Brain_extraction-b18e8797-786c-468f-8422-39c9a03c92b7.pklz b/...200902-170910-hkebiri-Multiple_Brain_extraction-b18e8797-786c-468f-8422-39c9a03c92b7.pklz
diff --git a/...200902-182548-hkebiri-Multiple_Brain_extraction-94bdeb49-6c0b-47f5-9a03-ddeb8f3fe5d8.pklz b/...200902-182548-hkebiri-Multiple_Brain_extraction-94bdeb49-6c0b-47f5-9a03-ddeb8f3fe5d8.pklz
diff --git a/pymialsrtk/interfaces/preprocess.py b/pymialsrtk/interfaces/preprocess.py
@@ -694,7 +694,8 @@ def _extractBrain(self, dataPath, modelCkptLoc, thresholdLoc, modelCkptSeg, thre
         img_nib = nibabel.load(os.path.join(dataPath))
         image_data = img_nib.get_data()
         images = np.zeros((image_data.shape[2], width, height, n_channels))
-        pred3dFinal = np.zeros((image_data.shape[2], width, height, n_channels))
+        #pred3dFinal = np.zeros((image_data.shape[2], width, height, n_channels))
+        pred3dFinal = np.zeros((image_data.shape[2], image_data.shape[0], image_data.shape[1], n_channels))
 
         slice_counter = 0
         for ii in range(image_data.shape[2]):
@@ -801,7 +802,7 @@ def _extractBrain(self, dataPath, modelCkptLoc, thresholdLoc, modelCkptSeg, thre
             for i in range(np.asarray(pred3d).shape[0]):
                 if np.sum(pred3d[i, :, :]) != 0:
                     pred3d[i, :, :] = self._extractLargestCC(pred3d[i, :, :].astype('uint8'))
-                    contours, _ = cv2.findContours(pred3d[i, :, :].astype('uint8'), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
+                    contours, hierarchy = cv2.findContours(pred3d[i, :, :].astype('uint8'), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
                     area = cv2.minAreaRect(np.squeeze(contours))
                     heights.append(area[1][0])
                     widths.append(area[1][1])