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Signed-off-by: neuronflow <florian.kofler@tum.de>
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Lines changed: 47 additions & 67 deletions

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‎BraTS-Toolkit/data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/normalized_bet/OtherEXampleFromTCIA_fla_bet_normalized.nii.gz‎

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‎BraTS-Toolkit/data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/normalized_bet/OtherEXampleFromTCIA_t1_bet_normalized.nii.gz‎

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‎BraTS-Toolkit/data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/normalized_bet/OtherEXampleFromTCIA_t1c_bet_normalized.nii.gz‎

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‎BraTS-Toolkit/data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/normalized_bet/OtherEXampleFromTCIA_t2_bet_normalized.nii.gz‎

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‎BraTS-Toolkit/data/TCGA-DU-7294/TCGA-DU-7294_brainles/normalized_bet/TCGA-DU-7294_fla_bet_normalized.nii.gz‎

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‎BraTS-Toolkit/data/TCGA-DU-7294/TCGA-DU-7294_brainles/normalized_bet/TCGA-DU-7294_t1_bet_normalized.nii.gz‎

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‎BraTS-Toolkit/data/TCGA-DU-7294/TCGA-DU-7294_brainles/normalized_bet/TCGA-DU-7294_t1c_bet_normalized.nii.gz‎

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‎BraTS-Toolkit/data/TCGA-DU-7294/TCGA-DU-7294_brainles/normalized_bet/TCGA-DU-7294_t2_bet_normalized.nii.gz‎

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‎BraTS-Toolkit/glioma_segmentation_with_BraTS_Toolkit.ipynb‎

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"metadata": {},
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"Requirement already satisfied: brainles_preprocessing in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (0.0.25)\n",
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"Collecting brainles_preprocessing\n",
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" Downloading brainles_preprocessing-0.0.26-py3-none-any.whl.metadata (3.0 kB)\n",
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"Requirement already satisfied: brats_toolkit in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (1.0.14)\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: nvidia-nvjitlink-cu12 in /home/florian/.local/lib/python3.10/site-packages (from nvidia-cusolver-cu12==11.4.5.107->torch>=0.4.1->BrainLes-HD-BET>=0.0.5->brainles_preprocessing) (12.3.52)\n",
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"Requirement already satisfied: MarkupSafe>=2.0 in /home/florian/.local/lib/python3.10/site-packages (from jinja2->torch>=0.4.1->BrainLes-HD-BET>=0.0.5->brainles_preprocessing) (2.1.3)\n",
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"Requirement already satisfied: mpmath>=0.19 in /home/florian/.local/lib/python3.10/site-packages (from sympy->torch>=0.4.1->BrainLes-HD-BET>=0.0.5->brainles_preprocessing) (1.3.0)\n",
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"Downloading brainles_preprocessing-0.0.26-py3-none-any.whl (19.7 MB)\n",
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"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m19.7/19.7 MB\u001b[0m \u001b[31m89.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m:00:01\u001b[0m00:01\u001b[0m\n",
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"\u001b[?25hInstalling collected packages: brainles_preprocessing\n",
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" Attempting uninstall: brainles_preprocessing\n",
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" Found existing installation: brainles_preprocessing 0.0.25\n",
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" Uninstalling brainles_preprocessing-0.0.25:\n",
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" Successfully uninstalled brainles_preprocessing-0.0.25\n",
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"Successfully installed brainles_preprocessing-0.0.26\n",
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"Note: you may need to restart the kernel to use updated packages.\n",
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"Requirement already satisfied: matplotlib in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (3.8.3)\n",
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"Requirement already satisfied: contourpy>=1.0.1 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from matplotlib) (1.2.0)\n",
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"Requirement already satisfied: pyparsing>=2.3.1 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from matplotlib) (3.1.1)\n",
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"Requirement already satisfied: python-dateutil>=2.7 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from matplotlib) (2.8.2)\n",
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"Requirement already satisfied: six>=1.5 in /home/florian/miniconda3/envs/aurora_tutorial/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib) (1.16.0)\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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"processing: /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/data/OtherEXampleFromTCIA\n",
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"*** start ***\n"
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"*** start ***\n",
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"File: /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/atlas-space/atlas__t1c.nii.gz\n",
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"preprocessing...\n",
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"image shape after preprocessing: (103, 160, 160)\n",
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"prediction (CNN id)...\n",
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"exporting segmentation...\n",
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"current image /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/brain-extraction/atlas_bet_t1c.nii.gz\n",
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"current image /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/brain-extraction/brain_masked/brain_masked__t1.nii.gz\n",
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"current image /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/brain-extraction/brain_masked/brain_masked__t2.nii.gz\n",
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"current image /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/brain-extraction/brain_masked/brain_masked__flair.nii.gz\n"
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" 50%|█████ | 1/2 [03:00<03:00, 180.99s/it]"
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" 50%|█████ | 1/2 [04:17<04:17, 257.19s/it]"
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"processing: /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/data/TCGA-DU-7294\n",
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"*** start ***\n"
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"*** start ***\n",
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"File: /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/atlas-space/atlas__t1c.nii.gz\n",
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"preprocessing...\n",
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"image shape after preprocessing: (103, 160, 160)\n",
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"prediction (CNN id)...\n",
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"0\n",
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"exporting segmentation...\n",
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"current image /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/brain-extraction/atlas_bet_t1c.nii.gz\n",
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"current image /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/brain-extraction/brain_masked/brain_masked__t1.nii.gz\n",
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"current image /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/brain-extraction/brain_masked/brain_masked__t2.nii.gz\n",
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"current image /home/florian/flow/BrainLesion/tutorials/BraTS-Toolkit/temporary_directory/brain-extraction/brain_masked/brain_masked__flair.nii.gz\n"
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"100%|██████████| 2/2 [09:48<00:00, 294.05s/it]\n"
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"100%|██████████| 2/2 [10:53<00:00, 326.56s/it]\n"
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‎preprocessing/data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c.nii.gz‎

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