├── LICENSE ├── README.md ├── TORTOISEV4 ├── CMakeLists.txt ├── README.md └── tools │ └── README.md ├── external_libraries └── bet │ └── Linux │ ├── betokan.h │ ├── libbetokan.a │ ├── libbetokan2.a │ └── libbetokan_orig.a ├── settings ├── defaults.dmc ├── mecc_settings │ ├── cubic.mec │ ├── cubic_isoc.mec │ ├── justeddy.mec │ ├── justeddy_isoc.mec │ ├── quadratic.mec │ ├── quadratic_isoc.mec │ └── rigid.mec ├── system_settings │ └── default_system_settings.json └── version.txt └── src ├── README.md ├── cuda_src ├── compute_entropy.cu ├── compute_entropy.cxx ├── compute_entropy.h ├── compute_metric.cu ├── compute_metric.cxx ├── compute_metric.h ├── compute_mi_cuda.cu ├── compute_mi_cuda.cxx ├── compute_mi_cuda.h ├── cuda_image.cxx ├── cuda_image.h ├── cuda_image_utilities.cu ├── cuda_image_utilities.cxx ├── cuda_image_utilities.h ├── cuda_utils.h ├── gaussian_smooth_image.cu ├── gaussian_smooth_image.cxx ├── gaussian_smooth_image.h ├── quadratic_transform_image.cu ├── quadratic_transform_image.cxx ├── quadratic_transform_image.h ├── register_dwi_to_b0_cuda.cxx ├── register_dwi_to_b0_cuda.h ├── register_dwi_to_slice_cuda.h ├── resample_image.cu ├── resample_image.cxx ├── resample_image.h ├── rigid_transform_image.cu ├── rigid_transform_image.cxx ├── rigid_transform_image.h ├── warp_image.cu ├── warp_image.cxx └── warp_image.h ├── external_src ├── cmpfit-1.3a │ ├── DISCLAIMER │ ├── Makefile │ ├── README │ ├── libmpfit.a │ ├── mpfit.c │ ├── mpfit.h │ ├── mpfit.o │ ├── testmpfit │ ├── testmpfit.c │ └── testmpfit.log └── json_nlohmann │ └── json.hpp ├── main ├── DIFFPREP.cxx ├── DIFFPREP.h ├── DRBUDDI.cxx ├── DRBUDDI.h ├── DRBUDDIBase.cxx ├── DRBUDDIBase.h ├── DRBUDDI_Diffeo.cxx ├── DRBUDDI_Diffeo.h ├── DiffusionModel.h ├── EPIREG.cxx ├── EPIREG.h ├── FINALDATA.cxx ├── FINALDATA.h ├── OmpThreadBase.h ├── TORTOISE.cxx ├── TORTOISE.h ├── TORTOISE_global.cxx ├── TORTOISE_parser.cxx ├── TORTOISE_parser.h ├── antsCommandLineOption.cxx ├── antsCommandLineOption.h ├── antsCommandLineParser.cxx ├── antsCommandLineParser.h ├── compute_metrics (copy).h ├── compute_metrics.h ├── compute_metrics_cc.h ├── compute_metrics_ccjacs.h ├── compute_metrics_ccsk.h ├── compute_metrics_msjac (copy).h ├── compute_metrics_msjac.h ├── create_mask.cxx ├── create_mask.h ├── defines.cxx ├── defines.h ├── drbuddi_image_utilities.cxx ├── drbuddi_image_utilities.h ├── drbuddi_structs.h ├── itkBSplineInterpolateImageFunctionOkan.h ├── itkBSplineInterpolateImageFunctionOkan.hxx ├── itkDIFFPREPGradientDescentOptimizer.cxx ├── itkDIFFPREPGradientDescentOptimizer.h ├── itkDIFFPREPGradientDescentOptimizerv4.cxx ├── itkDIFFPREPGradientDescentOptimizerv4.h ├── itkInvertDisplacementFieldImageFilterOkan.h ├── itkInvertDisplacementFieldImageFilterOkan.hxx ├── itkLinearInterpolateImageFunctionOkan.h ├── itkLinearInterpolateImageFunctionOkan.hxx ├── itkMattesMutualInformationImageToImageMetricv4Okan.h ├── itkMattesMutualInformationImageToImageMetricv4Okan.hxx ├── itkOkanImageRegistrationMethodv4.h ├── itkOkanImageRegistrationMethodv4.hxx ├── itkOkanQuadraticTransform.h ├── itkOkanQuadraticTransform.hxx ├── main.cxx ├── mecc_settings.h ├── register_dwi_to_b0.cxx ├── register_dwi_to_b0.h ├── register_dwi_to_slice.h ├── registration_settings.h ├── rigid_register_images.cxx ├── rigid_register_images.h ├── run_drbuddi_stage.cxx ├── run_drbuddi_stage.h ├── run_drbuddi_stage_TVVF.cxx └── run_drbuddi_stage_TVVF.h ├── tools ├── ApplyTransformationToScalar2 │ └── ApplyTransformationToScalar2.cxx ├── Combine3DImagesTo4D │ └── Combine3DImagesTo4D.cxx ├── CombineDWIs │ ├── combine_4dimages.cxx │ ├── combine_dwis_main.cxx │ ├── combine_dwis_with_bmatrix.h │ └── combine_dwis_with_bmatrix_main.cxx ├── CombineTransformations │ ├── combine_transformations.cxx │ ├── combine_transformations_with_output_name.cxx │ └── combine_transformations_with_reference.cxx ├── ComputeADMap │ └── compute_ad_map.cxx ├── ComputeDECMap │ ├── compute_dec_map.cxx │ ├── compute_dec_map_parser.cxx │ ├── compute_dec_map_parser.h │ ├── compute_wldec_map.cxx │ └── compute_wpdec_map.cxx ├── ComputeEigVecImage │ └── compute_eigvec_image.cxx ├── ComputeFAMap │ ├── compute_fa_map.cxx │ └── compute_fa_map.h ├── ComputeGlyphMaps │ ├── compute_glyph_maps (copy).cxx │ ├── compute_glyph_maps.cxx │ ├── vtkTensorGlyphOkan.cxx │ └── vtkTensorGlyphOkan.h ├── ComputeLIMap │ ├── compute_li_map.cxx │ └── compute_li_map.h ├── ComputeLineField │ └── ComputeLineField.cxx ├── ComputeMAPMRI_NG │ └── estimate_mapmri_ng.cxx ├── ComputeMAPMRI_PA │ └── estimate_mapmri_pa.cxx ├── ComputeMAPMRI_RTOP │ └── estimate_mapmri_rtop.cxx ├── ComputeMODEMap │ └── compute_mode_map.cxx ├── ComputeNSDECMap │ ├── compute_ns_dec_map.cxx │ ├── compute_ns_dec_map_original.cxx │ ├── compute_ns_dec_map_parser.cxx │ └── compute_ns_dec_map_parser.h ├── ComputeRDMap │ └── compute_rd_map.cxx ├── ComputeRTOPDTIMaps │ └── compute_rtop_dti_maps.cxx ├── ComputeSKMap │ └── compute_sk_map.cxx ├── ComputeTRMap │ └── compute_tr_map.cxx ├── ComputeWLMap │ ├── compute_wl_map.cxx │ └── compute_wl_map.h ├── ComputeWPMap │ ├── compute_wp_map.cxx │ └── compute_wp_map.h ├── ComputeWSMap │ └── compute_ws_map.cxx ├── Convert4DImageToDisplacementField │ └── Convert4DImageToDisplacementField.cxx ├── ConvertGEGradientsToBMatrix │ └── ConvertGEGradientsToBMatrix.cxx ├── ConvertLGradNonLinToDefField │ └── ConvertLGradNonLinToDefField.cxx ├── ConvertQuadraticTransformToDisplacementField │ └── convert_eddy_trans_to_field.hxx ├── CreateDummyJson │ ├── CreateDummyJson.cxx │ ├── CreateDummyJson_parser.cxx │ └── CreateDummyJson_parser.h ├── CreateGradientNonlinearityBMatrix │ ├── CreateGradientNonlinearityBMatrix.cxx │ ├── CreateGradientNonlinearityBMatrix_parser.cxx │ └── CreateGradientNonlinearityBMatrix_parser.h ├── CreateMask │ └── create_mask_main.cxx ├── CreateNonlinearityDisplacementMap │ └── mk_displacementMaps.cxx ├── DIFFPREPAnonymizer │ ├── diffprep_anonymizer.cxx │ ├── diffprep_anonymizer.h │ ├── itkGDCMImageIOOkan.cxx │ ├── itkGDCMImageIOOkan.h │ └── tag_list.txt ├── DRBUDDI │ ├── DRBUDDI_main.cxx │ ├── DRBUDDI_parserBase.cxx │ └── DRBUDDI_parserBase.h ├── DRTAMAS │ ├── ApplyTransformationToTensorDRT.cxx │ ├── DRTAMAS.cxx │ ├── DRTAMAS.h │ ├── DRTAMASRigid.cxx │ ├── DRTAMASRigid.h │ ├── DRTAMASRigid_Bulk.cxx │ ├── DRTAMASRigid_Bulk.h │ ├── DRTAMASRigid_main.cxx │ ├── DRTAMAS_Diffeo (copy).cxx │ ├── DRTAMAS_Diffeo.cxx │ ├── DRTAMAS_Diffeo.h │ ├── DRTAMAS_batch_register_to_target_main.bash │ ├── DRTAMAS_create_template_main.bash │ ├── DRTAMAS_main.cxx │ ├── DRTAMAS_parser.cxx │ ├── DRTAMAS_parser.h │ ├── DRTAMAS_utilities.cu │ ├── DRTAMAS_utilities.cxx │ ├── DRTAMAS_utilities.h │ ├── DRTAMAS_utilities_cp.cxx │ ├── DRTAMAS_utilities_cp.h │ ├── compute_metric_dev (another copy).cu │ ├── compute_metric_dev (copy).cu │ ├── compute_metric_dev.cu │ ├── compute_metric_dev.cxx │ ├── compute_metric_dev.h │ ├── drtamas_structs.h │ ├── run_drtamas_stage (copy).cxx │ ├── run_drtamas_stage.cxx │ ├── run_drtamas_stage.h │ ├── run_drtamas_stage_rigid.cxx │ ├── run_drtamas_stage_rigid.h │ └── select_most_representative_sample.cxx ├── DWIDenoise │ ├── dwi_denoise.cxx │ └── dwi_denoise.h ├── EstimateExperimentalDeviationScalar │ ├── estimate_experimental_deviation_scalar.cxx │ ├── estimate_experimental_deviation_scalar_parser.cxx │ ├── estimate_experimental_deviation_scalar_parser.h │ └── vnl_matrix_inverse.h ├── EstimateMAPMRI │ ├── MAPMRIModel.cxx │ ├── MAPMRIModel.h │ ├── bmat2q.h │ ├── compute_eigen_images.h │ ├── constrained_least_squares.h │ ├── estimate_mapmri.h │ ├── estimate_mapmri_main.cxx │ ├── estimate_mapmri_parser.cxx │ ├── estimate_mapmri_parser.h │ ├── fit_mapmri.h │ └── synthesize_dwi_from_mapmri.h ├── EstimateTensor │ ├── DTIModel.cxx │ ├── DTIModel.h │ ├── estimate_tensor_wlls.cxx │ ├── estimate_tensor_wlls.h │ ├── estimate_tensor_wlls_main.cxx │ ├── estimate_tensor_wlls_parser.cxx │ ├── estimate_tensor_wlls_parser.h │ └── synthesize_dwi_from_tensor.h ├── ExtractAllPNGsFromNIFTI │ └── extract_all_pngs_from_nifti.cxx ├── ExtractDWISubset │ ├── extract_dwi_subset.cxx │ ├── extract_dwi_subset_parser.cxx │ └── extract_dwi_subset_parser.h ├── ExtractImage │ ├── extract_component_from_itk_vector_image.cxx │ ├── extract_image.cxx │ ├── extract_image_parser.cxx │ └── extract_image_parser.h ├── ExtractPNGFromNIFTI │ └── extract_png_from_nifti.cxx ├── FitNIFTIIso │ ├── Fit_nifti_iso.cxx │ ├── Fit_nifti_iso.h │ ├── erodeMask.cxx │ ├── erodeMask.h │ ├── fit_nifti_iso_parser.cxx │ ├── fit_nifti_iso_parser.h │ ├── gradcal.cxx │ ├── gradcal.h │ ├── init_iso_gw.cxx │ ├── init_iso_gw.h │ ├── iso_gw.cxx │ ├── iso_gw.h │ ├── main.cxx │ ├── read_grad_cal.cxx │ └── read_grad_cal.h ├── FlipImage3D │ └── flip_image_3d.cxx ├── FlipImage4D │ └── flip_image_4d.cxx ├── FlipSwapBMatrix │ ├── FlipSwapBMatrix.cxx │ ├── FlipSwapBMatrix_parser.cxx │ ├── FlipSwapBMatrix_parser.h │ ├── antsCommandLineParser2.cxx │ └── antsCommandLineParser2.h ├── InvertTransformation │ └── invert_transformation.cxx ├── IsDirectionPositiveDet │ └── IsDirectionPositiveDet.cxx ├── MaskTensorWith3D │ └── MaskTensorWith3D.cxx ├── Pad4DImage │ ├── Pad3DImage.cxx │ └── Pad4DImage.cxx ├── PadImage │ └── pad_image.hxx ├── PrintHeaderT │ └── PrintHeader.cxx ├── ReorientImage │ ├── reorient_image.cxx │ ├── reorient_image.h │ ├── reorient_image_parser.cxx │ └── reorient_image_parser.h ├── ReorientImage3D │ ├── reorient_image3d.cxx │ ├── reorient_image_parser.cxx │ └── reorient_image_parser.h ├── ResampleDWIs │ ├── resample_dwis.cxx │ └── resample_dwis.h ├── RotateBMatrix │ ├── rotate_bmatrix.cxx │ ├── rotate_bmatrix.h │ └── rotate_bmatrix_main.cxx ├── SelectBestB0 │ ├── SelectBestB0_main.cxx │ └── select_best_b0.h ├── Set4DImageDirection │ └── set_4dimage_direction.cxx ├── Set4DImageOrigin │ └── set_4dimage_origin.cxx ├── Set4DImageResolution │ └── Set4DImageResolution.cxx ├── StdevImages3D │ └── stdev_images_3d.cxx ├── SynthesizeDWIFromMAPMRI │ ├── synthesize_dwi_from_map_test.cxx │ └── synthesize_dwis_from_mapmri.cxx ├── SynthesizeDWIsFromTensor │ └── synthesize_dwis_from_tensor.cxx ├── TORTOISEBMatrixToBT │ └── tortoise_bmatrix_to_bt.cxx ├── TORTOISEBmatrixToFSLBVecs │ ├── fsl_bvecs_tortoise_bmatrix.cxx │ ├── tortoise_bmatrix_to_fsl_bvecs.cxx │ └── tortoise_bmatrix_to_fsl_bvecs.h ├── UnObliqueImage │ └── UnObliqueImage.cxx ├── UnRing │ ├── gibbs_main.cxx │ └── unring.h ├── Vol2SlRegistration │ └── vol2sl_registration_main.cxx ├── ZeroSlices3D │ └── ZeroSlices3D.cxx ├── gradnonlin │ ├── gradcal.cxx │ ├── gradcal.h │ ├── init_iso_gw.cxx │ ├── init_iso_gw.h │ ├── mk_displacementMaps.cxx │ └── mk_displacementMaps.h └── import_bruker │ ├── ImportBruker.cxx │ ├── bruker_anatomical_parser (copy).cxx │ ├── bruker_anatomical_parser (copy).h │ ├── bruker_anatomical_parser.cxx │ ├── bruker_anatomical_parser.h │ ├── bruker_parser.cxx │ ├── bruker_parser.h │ ├── convert_bruker.cxx │ ├── convert_bruker.h │ ├── 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