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Author: brainless-bot[bot]

preprocessing/preprocessing_tutorial.ipynb

@@ -160,7 +160,9 @@
     "from brainles_preprocessing.modality import Modality, CenterModality\n",
     "from brainles_preprocessing.preprocessor import Preprocessor\n",
     "from brainles_preprocessing.registration import ANTsRegistrator\n",
-    "from brainles_preprocessing.normalization.percentile_normalizer import PercentileNormalizer\n",
+    "from brainles_preprocessing.normalization.percentile_normalizer import (\n",
+    "    PercentileNormalizer,\n",
+    ")\n",
     "\n",
     "import utils"
    ]
@@ -191,7 +193,7 @@
     "t1c_normalized_bet_output_path = output_dir / \"t1c_normalized_bet.nii.gz\"\n",
     "t1c_normalized_defaced_output_path = output_dir / \"t1c_normalized_defaced.nii.gz\"\n",
     "t1c_bet_mask = output_dir / \"t1c_bet_mask.nii.gz\"\n",
-    "t1c_defacing_mask = output_dir / \"t1c_defacing_mask.nii.gz\" \n",
+    "t1c_defacing_mask = output_dir / \"t1c_defacing_mask.nii.gz\"\n",
     "\n",
     "t1_normalized_bet_output_path = output_dir / \"t1_normalized_bet.nii.gz\"\n",
     "fla_normalized_bet_output_path = output_dir / \"fla_normalized_bet.nii.gz\"\n",
@@ -446,10 +448,25 @@
    ],
    "source": [
     "# inspect the different outputs for the center modality (normalized atlas registered with skull, brain extracted (bet) and defaced)\n",
-    "utils.visualize_data(files=[t1c_normalized_skull_output_path, t1c_normalized_bet_output_path, t1c_normalized_defaced_output_path], label=\"T1C outputs\")\n",
+    "utils.visualize_data(\n",
+    "    files=[\n",
+    "        t1c_normalized_skull_output_path,\n",
+    "        t1c_normalized_bet_output_path,\n",
+    "        t1c_normalized_defaced_output_path,\n",
+    "    ],\n",
+    "    label=\"T1C outputs\",\n",
+    ")\n",
     "\n",
     "# inspect the different outputs for the all modalities (normalized atlas registered brain extracted (bet))\n",
-    "utils.visualize_data(files=[t1c_normalized_bet_output_path, t1_normalized_bet_output_path, fla_normalized_bet_output_path, t2_normalized_bet_output_path], label=\"BET outputs\")\n",
+    "utils.visualize_data(\n",
+    "    files=[\n",
+    "        t1c_normalized_bet_output_path,\n",
+    "        t1_normalized_bet_output_path,\n",
+    "        fla_normalized_bet_output_path,\n",
+    "        t2_normalized_bet_output_path,\n",
+    "    ],\n",
+    "    label=\"BET outputs\",\n",
+    ")\n",
     "\n",
     "# showcase the defacing result from a more suitable angle\n",
     "utils.visualize_defacing(file=t1c_normalized_defaced_output_path)"