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‎preprocessing/preprocessing_tutorial.ipynb‎

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"text": [
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"Requirement already satisfied: brainles_preprocessing in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (0.0.23)\n",
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"Requirement already satisfied: brats_toolkit in /home/florian/.local/lib/python3.10/site-packages (1.0.11)\n",
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"Requirement already satisfied: brainles_preprocessing in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (0.0.24)\n",
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"Requirement already satisfied: auxiliary in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (0.0.40)\n",
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"Requirement already satisfied: BrainLes-HD-BET>=0.0.5 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from brainles_preprocessing) (0.0.5)\n",
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"Requirement already satisfied: nibabel<4.0.0,>=3.2.1 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from brainles_preprocessing) (3.2.2)\n",
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"Requirement already satisfied: rich<14.0.0,>=13.6.0 in /home/florian/.local/lib/python3.10/site-packages (from brainles_preprocessing) (13.7.0)\n",
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"Requirement already satisfied: tqdm<5.0.0,>=4.64.1 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from brainles_preprocessing) (4.66.1)\n",
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"Requirement already satisfied: ttictoc<0.6.0,>=0.5.6 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from brainles_preprocessing) (0.5.6)\n",
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"Requirement already satisfied: SimpleITK<3.0.0,>=2.3.1 in /home/florian/.local/lib/python3.10/site-packages (from brats_toolkit) (2.3.1)\n",
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"Requirement already satisfied: python-engineio<4.0.0,>=3.14.2 in /home/florian/.local/lib/python3.10/site-packages (from brats_toolkit) (3.14.2)\n",
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"Requirement already satisfied: python-socketio<5.0.0,>=4.6.1 in /home/florian/.local/lib/python3.10/site-packages (from brats_toolkit) (4.6.1)\n",
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"Requirement already satisfied: requests<3.0.0,>=2.24.0 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from brats_toolkit) (2.31.0)\n",
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"Requirement already satisfied: pillow>=10.0.0 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from auxiliary) (10.2.0)\n",
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"Requirement already satisfied: tifffile>=2023.8.25 in /home/florian/.local/lib/python3.10/site-packages (from auxiliary) (2023.12.9)\n",
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"Requirement already satisfied: torch>=0.4.1 in /home/florian/.local/lib/python3.10/site-packages (from BrainLes-HD-BET>=0.0.5->brainles_preprocessing) (2.1.2)\n",
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"Requirement already satisfied: scikit-image>=0.21.0 in /home/florian/.local/lib/python3.10/site-packages (from BrainLes-HD-BET>=0.0.5->brainles_preprocessing) (0.22.0)\n",
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"Requirement already satisfied: SimpleITK>=2.2.1 in /home/florian/.local/lib/python3.10/site-packages (from BrainLes-HD-BET>=0.0.5->brainles_preprocessing) (2.3.1)\n",
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"Requirement already satisfied: packaging>=14.3 in /home/florian/.local/lib/python3.10/site-packages (from nibabel<4.0.0,>=3.2.1->brainles_preprocessing) (23.2)\n",
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"Requirement already satisfied: setuptools in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from nibabel<4.0.0,>=3.2.1->brainles_preprocessing) (68.2.2)\n",
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"Requirement already satisfied: six>=1.9.0 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from python-engineio<4.0.0,>=3.14.2->brats_toolkit) (1.16.0)\n",
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"Requirement already satisfied: charset-normalizer<4,>=2 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from requests<3.0.0,>=2.24.0->brats_toolkit) (3.3.2)\n",
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"Requirement already satisfied: idna<4,>=2.5 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from requests<3.0.0,>=2.24.0->brats_toolkit) (3.6)\n",
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"Requirement already satisfied: urllib3<3,>=1.21.1 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from requests<3.0.0,>=2.24.0->brats_toolkit) (2.2.0)\n",
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"Requirement already satisfied: certifi>=2017.4.17 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from requests<3.0.0,>=2.24.0->brats_toolkit) (2024.2.2)\n",
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"Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from matplotlib) (3.1.1)\n",
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"Note: you may need to restart the kernel to use updated packages.\n",
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"The autoreload extension is already loaded. To reload it, use:\n",
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" %reload_ext autoreload\n"
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"Note: you may need to restart the kernel to use updated packages.\n"
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"\n",
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"from brainles_preprocessing.brain_extraction import HDBetExtractor\n",
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"from brainles_preprocessing.modality import Modality\n",
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"from brainles_preprocessing.preprocessor import Preprocessor, PreprocessorGPU\n",
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"from brainles_preprocessing.preprocessor import Preprocessor\n",
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"from brainles_preprocessing.registration import NiftyRegRegistrator\n",
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"\n",
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"\n",
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"def preprocess(inputDir):\n",
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"def preprocess_exam_in_brats_style(inputDir: str) -> None:\n",
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" \"\"\"\n",
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" Perform BRATS (Brain Tumor Segmentation) style preprocessing on MRI exam data.\n",
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"\n",
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" Args:\n",
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" inputDir (str): Path to the directory containing raw MRI files for an exam.\n",
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"\n",
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" Raises:\n",
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" Exception: If any error occurs during the preprocessing.\n",
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"\n",
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" Example:\n",
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" brat_style_preprocess_exam(\"/path/to/exam_directory\")\n",
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"\n",
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" This function preprocesses MRI exam data following the BRATS style, which includes the following steps:\n",
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" 1. Normalization using a percentile normalizer.\n",
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" 2. Registration and correction using NiftyReg.\n",
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" 3. Brain extraction using HDBet.\n",
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"\n",
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" The processed data is saved in a structured directory within the input directory.\n",
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"\n",
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" Args:\n",
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" inputDir (str): Path to the directory containing raw MRI files for an exam.\n",
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"\n",
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" Returns:\n",
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" None\n",
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" \"\"\"\n",
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" inputDir = turbopath(inputDir)\n",
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" try:\n",
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" print(\"*** start ***\")\n",
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" moving_modalities=moving_modalities,\n",
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" registrator=NiftyRegRegistrator(),\n",
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" brain_extractor=HDBetExtractor(),\n",
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" # temp_folder=\"tempo\",\n",
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" limit_cuda_visible_devices=\"1\",\n",
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" # optional: we provide a temporary directory as a sandbox for the preprocessin\n",
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" temp_folder=\"temporary_directory\",\n",
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" limit_cuda_visible_devices=\"0\",\n",
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" )\n",
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"\n",
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" preprocessor.run(\n",
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},
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"\n",
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"for exam in tqdm(exams):\n",
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" print(\"processing:\", exam)\n",
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" brat_style_preprocess_exam(exam)"
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" preprocess_exam_in_brats_style(exam)"
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]
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}
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],

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