├── .gitignore ├── LICENSE.md ├── README.md ├── data ├── README.txt └── checkerboard.png ├── developers-scripts ├── BULLSEYE_Unbiased_LowRank_Atlas_Building.py ├── Low_Rank_Atlas_Iter_BRATS.py ├── Low_Rank_Atlas_Iter_BULLSEYE.py ├── eval_utils │ ├── TissueStatisticsValidation.py │ ├── affineAlighAllModalityImage.py │ ├── bsplineRegisterBRATSWithHealthyAtlas.py │ ├── deformSparseImages.py │ ├── measureSparityError.py │ ├── plotLowRankIteration.py │ ├── visDVF.py │ └── visIterationForOneSubject.py ├── run_greedy_LRA_BRATS.py ├── run_segmentation.py ├── test_ANTS_registration_BRATS.py ├── test_ANTS_registration_simulation.py └── unbiased_low_rank_atlas_building_bspline.py ├── examples ├── BRATS_data_notebooks │ ├── BRATS_PRCA_2D.ipynb │ ├── BRATS_PRCA_3D.ipynb │ ├── BRATS_PRCA_BullEyesSimulation.ipynb │ ├── BRATS_PRCA_challange_2D_Flair.ipynb │ ├── BRATS_PRCA_challange_2D_T1-test-for_iter.ipynb │ ├── BRATS_PRCA_challange_2D_T1.ipynb │ ├── FLAIR_FILES.txt │ ├── GT_FILES.txt │ ├── Low_Rank_Atlas_Iter_BRATS.ipynb │ ├── compareLABresults-2.ipynb │ ├── compareLABresults-Copy0.ipynb │ ├── compareLABresults-final.ipynb │ └── skullstripping.ipynb ├── configuration_files │ ├── BRATS2_Training_Data_8Inputs.txt │ ├── LAB_BRATS2_Training_Data_16Inputs.txt │ ├── LAB_BRATS2_Training_Data_8Inputs.txt │ ├── LAB_BRATS2_Training_Data_8Inputs_T1c.txt │ ├── LAB_BRATS2_Training_Data_8Inputs_T2.txt │ ├── LAB_BRATS_Synthetic_Data_20Inputs.txt │ ├── LAB_BRATS_Synthetic_Data_20Inputs_T1.txt │ ├── LAB_BRATS_Synthetic_Data_8Inputs.txt │ ├── LAB_BRATS_Synthetic_Data_8Inputs_T1.txt │ ├── LAB_BRATS_Synthetic_Data_T1_5Inputs.txt │ ├── LAB_BrainWeb_T1_5Inputs.txt │ ├── LAB_Simulation.txt │ ├── SoftwareConfiguration.txt │ ├── UAB_BRATS2_Training_Data_8Inputs.txt │ ├── UAB_BRATS_Synthetic_Data_20Inputs_T1.txt │ ├── UAB_BRATS_Synthetic_Data_8Inputs.txt │ ├── UAB_BRATS_Synthetic_Data_8Inputs_T1.txt │ └── UAB_BrainWebT1_5inputs.txt ├── ex1.py ├── faces_data_notebooks │ ├── LAB_2D_Face.ipynb │ ├── LAB_2D_Face_female_100inputs.ipynb │ ├── LAB_2D_Face_female_10inputs.ipynb │ └── LAB_2D_Face_female_20inputs.ipynb └── simulated_data_notebooks │ ├── BULLSEYE_Unbiased_Atlas_Building.ipynb │ ├── LAB_2D_Simulation-ForwardMapping.ipynb │ ├── LAB_2D_Simulation-test_longitudinal.ipynb │ ├── LAB_2D_Simulation.ipynb │ ├── LAB_2D_Simulation_varing_corruption.ipynb │ ├── LAR_2D_Bullseye.ipynb │ ├── Low_Rank_Atlas_Iter_Bullseye_3D.ipynb │ ├── PRCA_BullEyesSimulation.ipynb │ ├── gen_2D_simulation_data.ipynb │ └── pyrpca-Tutorial.ipynb ├── helper ├── gen_2D_simulation_data.py └── gen_3D_simulation_data.py ├── pyLAR ├── __init__.py ├── alm │ ├── __init__.py │ ├── ealm.py │ ├── ialm.py │ ├── op.py │ └── tests │ │ ├── im_baseline.dat │ │ ├── im_outliers.dat │ │ ├── test_ealm.py │ │ └── test_ialm.py ├── lra │ ├── __init__.py │ ├── batch.py │ ├── files.py │ ├── images.py │ ├── lr.py │ ├── nglra.py │ ├── registration.py │ ├── robust_pca.py │ ├── statistics.py │ ├── tests │ │ ├── __init__.py │ │ ├── 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