├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── question.md └── workflows │ ├── autoformat.yml │ ├── pr-lint.yml │ ├── release.yml │ └── tests.yml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── brainles_preprocessing ├── __init__.py ├── brain_extraction │ ├── __init__.py │ ├── brain_extractor.py │ └── synthstrip.py ├── brats │ ├── __init__.py │ ├── t1_centric.py │ └── t1c_centric.py ├── cli.py ├── constants.py ├── defacing │ ├── __init__.py │ ├── defacer.py │ └── quickshear │ │ ├── __init__.py │ │ ├── nipy_quickshear.py │ │ └── quickshear.py ├── modality.py ├── n4_bias_correction │ ├── __init__.py │ ├── n4_bias_corrector.py │ └── sitk │ │ ├── __init__.py │ │ └── sitk_n4_bias_corrector.py ├── normalization │ ├── __init__.py │ ├── normalizer_base.py │ ├── percentile_normalizer.py │ └── windowing_normalizer.py ├── preprocessor │ ├── __init__.py │ ├── atlas_centric_preprocessor.py │ ├── native_space_preprocessor.py │ └── preprocessor.py ├── registration │ ├── ANTs │ │ ├── ANTs.py │ │ ├── TODO_ANTs_parameters.py │ │ └── __init__.py │ ├── __init__.py │ ├── elastix │ │ ├── __init__.py │ │ └── elastix.py │ ├── greedy │ │ ├── __init__.py │ │ └── greedy.py │ ├── niftyreg │ │ ├── __init__.py │ │ ├── niftyreg.py │ │ └── niftyreg_scripts │ │ │ ├── niftyreg_1.5.68 │ │ │ ├── bin │ │ │ │ ├── groupwise_niftyreg_params.sh │ │ │ │ ├── groupwise_niftyreg_run.sh │ │ │ │ ├── reg_aladin │ │ │ │ ├── reg_average │ │ │ │ ├── reg_f3d │ │ │ │ ├── reg_jacobian │ │ │ │ ├── reg_measure │ │ │ │ ├── reg_resample │ │ │ │ ├── reg_tools │ │ │ │ └── reg_transform │ │ │ └── include │ │ │ │ ├── AffineDeformationFieldKernel.h │ │ │ │ ├── AladinContent.h │ │ │ │ ├── BlockMatchingKernel.h │ │ │ │ ├── CPUAffineDeformationFieldKernel.h │ │ │ │ ├── CPUBlockMatchingKernel.h │ │ │ │ ├── CPUConvolutionKernel.h │ │ │ │ ├── CPUKernelFactory.h │ │ │ │ ├── CPUOptimiseKernel.h │ │ │ │ ├── CPUResampleImageKernel.h │ │ │ │ ├── ConvolutionKernel.h │ │ │ │ ├── Kernel.h │ │ │ │ ├── KernelFactory.h │ │ │ │ ├── OptimiseKernel.h │ │ │ │ ├── Platform.h │ │ │ │ ├── ResampleImageKernel.h │ │ │ │ ├── _reg_ReadWriteImage.h │ │ │ │ ├── _reg_ReadWriteMatrix.h │ │ │ │ ├── _reg_aladin.cpp │ │ │ │ ├── _reg_aladin.h │ │ │ │ ├── _reg_aladin_sym.cpp │ │ │ │ ├── _reg_aladin_sym.h │ │ │ │ ├── _reg_base.h │ │ │ │ ├── _reg_blockMatching.h │ │ │ │ ├── _reg_dti.h │ │ │ │ ├── _reg_f3d.h │ │ │ │ ├── _reg_f3d2.h │ │ │ │ ├── _reg_f3d_sym.h │ │ │ │ ├── _reg_femTrans.h │ │ │ │ ├── _reg_globalTrans.h │ │ │ │ ├── _reg_kld.h │ │ │ │ ├── _reg_lncc.h │ │ │ │ ├── _reg_localTrans.h │ │ │ │ ├── _reg_localTrans_jac.h │ │ │ │ ├── _reg_localTrans_regul.h │ │ │ │ ├── _reg_macros.h │ │ │ │ ├── _reg_maths.h │ │ │ │ ├── _reg_maths_eigen.h │ │ │ │ ├── _reg_measure.h │ │ │ │ ├── _reg_mind.h │ │ │ │ ├── _reg_nmi.h │ │ │ │ ├── _reg_optimiser.cpp │ │ │ │ ├── _reg_optimiser.h │ │ │ │ ├── _reg_resampling.h │ │ │ │ ├── _reg_splineBasis.h │ │ │ │ ├── _reg_ssd.h │ │ │ │ ├── _reg_stringFormat.h │ │ │ │ ├── _reg_tools.h │ │ │ │ ├── nifti1.h │ │ │ │ ├── nifti1_io.h │ │ │ │ ├── png.h │ │ │ │ ├── pngconf.h │ │ │ │ ├── pngdebug.h │ │ │ │ ├── pnginfo.h │ │ │ │ ├── pnglibconf.h │ │ │ │ ├── pngpriv.h │ │ │ │ ├── pngstruct.h │ │ │ │ ├── readpng.h │ │ │ │ ├── reg_png.h │ │ │ │ ├── zlib.h │ │ │ │ ├── znzlib.h │ │ │ │ └── zutil.h │ │ │ ├── reg_aladin │ │ │ ├── reg_resample │ │ │ ├── rigid_reg.sh │ │ │ └── transform.sh │ └── registrator.py ├── transform.py └── utils │ ├── __init__.py │ ├── citation_reminder.py │ ├── generic.py │ └── zenodo.py ├── docs ├── Makefile ├── make.bat └── source │ ├── brain-extraction.rst │ ├── brainles-preprocessing.rst │ ├── conf.py │ ├── defacing.rst │ ├── index.rst │ ├── n4-bias-correction.rst │ └── registration.rst ├── example ├── example_atlas_centric_preprocessor.py ├── example_data │ ├── OtherEXampleFromTCIA │ │ ├── MRHR_FLAIR_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_FLAIR_AX_SE_IR_5_tir2d1_21_fla.nii.gz │ │ ├── MRHR_T1_AX_POST_GAD_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T1_AX_POST_GAD_SE_13_se2d1r_t1c.nii.gz │ │ ├── MRHR_T2_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T2_AX_SE_2_tse2d1_11_t2.nii.gz │ │ └── T1_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_T1_AX_SE_10_se2d1_t1.nii.gz │ └── TCGA-DU-7294 │ │ ├── AXIAL_FLAIR_RF2_150_TCGA-DU-7294_TCGA-DU-7294_GE_TCGA-DU-7294_AXIAL_FLAIR_RF2_150_IR_7_fla.nii.gz │ │ ├── AX_T1_POST_GD_FLAIR_TCGA-DU-7294_TCGA-DU-7294_GE_TCGA-DU-7294_AX_T1_POST_GD_FLAIR_RM_13_t1c.nii.gz │ │ ├── AX_T1_pre_gd_TCGA-DU-7294_TCGA-DU-7294_GE_TCGA-DU-7294_AX_T1_pre_gd_RM_8_t1.nii.gz │ │ └── AX_T2_FR-FSE_RF2_150_TCGA-DU-7294_TCGA-DU-7294_GE_TCGA-DU-7294_AX_T2_FR-FSE_RF2_150_RM_4_t2.nii.gz └── example_native_space_preprocessor.py ├── pyproject.toml └── tests ├── registrator_base.py ├── test_data └── input │ ├── ants_matrix.mat │ ├── bet_tcia_example_t1c_mask.nii.gz │ ├── ereg_matrix.mat │ ├── niftyreg_matrix.txt │ ├── tcia_example_t1.nii.gz │ └── 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