Merge pull request #66 from BrainLesion/65-bug-the-center-modality-is-not-skullstripped

65-bug-the-center-modality-is-not-skullstripped

Author: neuronflow

brainles_preprocessing/modality.py

@@ -98,11 +98,15 @@ def __init__(
         else:
             self.normalized_skull_output_path = normalized_skull_output_path
 
+        # print("self.raw_bet_output_path", self.raw_bet_output_path)
+        # print("self.normalized_skull_output_path", self.normalized_skull_output_path)
+        # print("self.bet:", self.bet)
+
     @property
     def bet(self) -> bool:
         return any(
             path is not None
-            for path in [self.raw_bet_output_path, self.normalized_skull_output_path]
+            for path in [self.raw_bet_output_path, self.normalized_bet_output_path]
         )
 
     def normalize(
@@ -290,6 +294,7 @@ def save_current_image(
             )
         elif normalization is True:
             image = read_nifti(self.current)
+            print("current image", self.current)
             normalized_image = self.normalizer.normalize(image=image)
             write_nifti(
                 input_array=normalized_image,

brainles_preprocessing/preprocessor.py

@@ -216,6 +216,7 @@ def run(
 
         # Optional: Brain extraction
         brain_extraction = any(modality.bet for modality in self.all_modalities)
+        # print("brain extraction: ", brain_extraction)
 
         if brain_extraction:
             bet_dir = os.path.join(self.temp_folder, "brain-extraction")