diff --git a/brainles_preprocessing/modality.py b/brainles_preprocessing/modality.py index 94bb669..042b009 100644 --- a/brainles_preprocessing/modality.py +++ b/brainles_preprocessing/modality.py @@ -119,7 +119,7 @@ def register( registrator.register( fixed_image_path=fixed_image_path, moving_image_path=self.current, - transformed_image=registered, + transformed_image_path=registered, matrix_path=registered_matrix, log_file_path=registered_log, ) diff --git a/brainles_preprocessing/registration/__init__.py b/brainles_preprocessing/registration/__init__.py index ab86e04..6f56b85 100644 --- a/brainles_preprocessing/registration/__init__.py +++ b/brainles_preprocessing/registration/__init__.py @@ -1 +1 @@ -from .niftyreg import NiftyRegRegistrator +from .niftyreg.niftyreg import NiftyRegRegistrator diff --git a/brainles_preprocessing/registration/niftyreg/__init__.py b/brainles_preprocessing/registration/niftyreg/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/brainles_preprocessing/registration/niftyreg.py b/brainles_preprocessing/registration/niftyreg/niftyreg.py similarity index 100% rename from brainles_preprocessing/registration/niftyreg.py rename to brainles_preprocessing/registration/niftyreg/niftyreg.py diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.cpp b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.cpp similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.cpp rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.cpp diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.cpp b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.cpp similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.cpp rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.cpp diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_blockMatching.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_blockMatching.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_blockMatching.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_blockMatching.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_dti.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_dti.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_dti.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_dti.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d2.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d2.h similarity index 100% rename from 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brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_femTrans.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_globalTrans.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_globalTrans.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_globalTrans.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_globalTrans.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_kld.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_kld.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_kld.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_kld.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_lncc.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_lncc.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_lncc.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_lncc.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_jac.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_jac.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_jac.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_jac.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_regul.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_regul.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_regul.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_regul.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_macros.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_macros.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_macros.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_macros.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths_eigen.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths_eigen.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths_eigen.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_maths_eigen.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_measure.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_measure.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_measure.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_measure.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_mind.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_mind.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_mind.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_mind.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_resampling.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_resampling.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_resampling.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_resampling.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_splineBasis.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_splineBasis.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_splineBasis.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_splineBasis.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ssd.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ssd.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ssd.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ssd.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_stringFormat.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_stringFormat.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_stringFormat.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_stringFormat.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/png.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/png.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/png.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/png.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/reg_aladin b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/reg_aladin similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/reg_aladin rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/reg_aladin diff --git a/brainles_preprocessing/registration/niftyreg_scripts/reg_resample b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/reg_resample similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/reg_resample rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/reg_resample diff --git a/brainles_preprocessing/registration/niftyreg_scripts/rigid_reg.sh b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/rigid_reg.sh similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/rigid_reg.sh rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/rigid_reg.sh diff --git a/brainles_preprocessing/registration/niftyreg_scripts/transform.sh b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/transform.sh similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/transform.sh rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/transform.sh diff --git a/tests/test_niftyreg_registrator.py b/tests/test_niftyreg_registrator.py index 2315960..94bcaca 100644 --- a/tests/test_niftyreg_registrator.py +++ b/tests/test_niftyreg_registrator.py @@ -4,7 +4,7 @@ from auxiliary.turbopath import turbopath -from brainles_preprocessing.registration.niftyreg import NiftyRegRegistrator +from brainles_preprocessing.registration.niftyreg.niftyreg import NiftyRegRegistrator class TestNiftyRegRegistrator(unittest.TestCase):