.gitignore
LICENSE
README.md
environment.yml
pyproject.toml
.github/workflows/build-test-env.yml
.github/workflows/draft-pdf.yml
.github/workflows/python-publish.yml
examples/Automatic_Contour.ipynb
examples/Bone_Mineral_Density.ipynb
examples/Finger_Joint_Comparison.ipynb
examples/Laplace_Hamming_Filter.ipynb
examples/Thickness_Of_Shapes.ipynb
examples/Trabecular_Segmentation.ipynb
examples/images/AUTOCONTOUR_IPL.nii
examples/images/GRAY_JOINT.nii
examples/images/IPL_JSW_DT_IMAGE.png
examples/images/IPL_vs_ORMIR_XCT_JOINT.nii
examples/images/TRAB_SEG_IPL.nii
examples/images/autocontour4.nii
examples/images/test1.nii
examples/images/test2.nii
manuscript/paper.bib
manuscript/paper.md
manuscript/figures/DT_Figure.png
manuscript/figures/DT_Figure_PY.png
manuscript/figures/IPL_vs_ORMIR_XCT-BMD.png
manuscript/figures/IPL_vs_ORMIR_XCT-BMD_PY.png
manuscript/figures/IPL_vs_ORMIR_XCT-DT.png
manuscript/figures/IPL_vs_ORMIR_XCT-DT_PY.png
manuscript/figures/Table1.png
manuscript/figures/Table2.png
manuscript/notebooks/JOSS_manuscript_Figure1.ipynb
manuscript/notebooks/JOSS_manuscript_Figure2_3.ipynb
manuscript/notebooks/JOSS_manuscript_Table1_2.ipynb
manuscript/notebooks/LinearRegression.py
manuscript/notebooks/joss_plots.py
manuscript/notebooks/csv/F_CYL_JSW_THICKNESS_IPL.csv
manuscript/notebooks/csv/F_CYL_OVERSAMPLE_SKEL_DT_THICKNESS_PY.csv
manuscript/notebooks/csv/F_SPH_JSW_THICKNESS_IPL.csv
manuscript/notebooks/csv/F_SPH_OVERSAMPLE_SKEL_DT_THICKNESS_PY.csv
manuscript/notebooks/csv/H_CYL_JSW_THICKNESS_IPL.csv
manuscript/notebooks/csv/H_CYL_OVERSAMPLE_SKEL_DT_THICKNESS_PY.csv
manuscript/notebooks/csv/H_SPH_JSW_THICKNESS_IPL.csv
manuscript/notebooks/csv/H_SPH_OVERSAMPLE_SKEL_DT_THICKNESS_PY.csv
manuscript/notebooks/csv/PLATE_JSW_THICKNESS_IPL.csv
manuscript/notebooks/csv/PLATE_OVERSAMPLE_SKEL_DT_THICKNESS_PY.csv
manuscript/notebooks/csv/autocontour.csv
manuscript/notebooks/csv/bmd_ipl.csv
manuscript/notebooks/csv/bmd_py.csv
manuscript/notebooks/csv/ipl_seg.csv
manuscript/notebooks/images/TEST_JOINT.nii
ormir_xct/__init__.py
ormir_xct.egg-info/PKG-INFO
ormir_xct.egg-info/SOURCES.txt
ormir_xct.egg-info/dependency_links.txt
ormir_xct.egg-info/entry_points.txt
ormir_xct.egg-info/requires.txt
ormir_xct.egg-info/top_level.txt
ormir_xct/core/__init__.py
ormir_xct/core/joint_space_analysis/README.md
ormir_xct/core/joint_space_analysis/__init__.py
ormir_xct/core/joint_space_analysis/jsw_morphometry.py
ormir_xct/core/microarchitecture/README.md
ormir_xct/core/microarchitecture/__init__.py
ormir_xct/core/microarchitecture/bmd.py
ormir_xct/core/microarchitecture/bmd_masked.py
ormir_xct/core/microarchitecture/trabecular_microarchitecture.py
ormir_xct/core/segmentation/README.md
ormir_xct/core/segmentation/__init__.py
ormir_xct/core/segmentation/adaptive_local_threshold.py
ormir_xct/core/segmentation/fft_laplace_hamming.py
ormir_xct/core/segmentation/seg_gauss.py
ormir_xct/core/segmentation/autocontour/AutocontourKnee.py
ormir_xct/core/segmentation/autocontour/__init__.py
ormir_xct/core/segmentation/autocontour/autocontour.py
ormir_xct/core/segmentation/autocontour/autocontour_gobj.py
ormir_xct/core/util/README.md
ormir_xct/core/util/__init__.py
ormir_xct/core/util/batch_file_converter.py
ormir_xct/core/util/connected_check.py
ormir_xct/core/util/file_converter.py
ormir_xct/core/util/file_reader.py
ormir_xct/core/util/generate_shapes.py
ormir_xct/core/util/hildebrand_thickness.py
ormir_xct/core/util/hrpqct_rescale.py
ormir_xct/core/util/image_to_dicom.py
ormir_xct/core/util/process_ipl_log.py
ormir_xct/core/util/process_py_log.py
ormir_xct/core/util/scrub_vms_extension.py
ormir_xct/core/util/seg_eval.py
ormir_xct/core/util/segmentation_evaluation.py
ormir_xct/core/util/sitk_itk.py
ormir_xct/core/util/sitk_vtk.py
ormir_xct/workflows/__init__.py
ormir_xct/workflows/adaptive_local_threshold_workflow.py
ormir_xct/workflows/autocontour_gobj_workflow.py
ormir_xct/workflows/autocontour_workflow.py
ormir_xct/workflows/bmd_masked_workflow.py
ormir_xct/workflows/bmd_workflow.py
ormir_xct/workflows/fft_laplace_hamming_workflow.py
ormir_xct/workflows/jsw_analysis_workflow.py
ormir_xct/workflows/seg_gauss_workflow.py
ormir_xct/workflows/trab_bvtv_workflow.py
ormir_xct/workflows/trab_microarchitecture_workflow.py
ormir_xct/workflows/trab_sp_workflow.py
ormir_xct/workflows/trab_th_workflow.py
ormir_xct/workflows/workflows.md
tests/__init__.py
tests/autocontour/__init__.py
tests/autocontour/test_autocontour.py
tests/bone_mineral_density/__init__.py
tests/bone_mineral_density/test_bone_mineral_density.py
tests/bone_mineral_density/test_bone_mineral_density_masked.py
tests/data/test_aim.AIM
tests/data/test_isq.ISQ
tests/data/test_joint.nii
tests/data/test_joint_mask.nii
tests/data/test_mha.mha
tests/data/test_nii.nii
tests/data/test_nrrd.nrrd
tests/data/test_dicom/IMG0001.dcm
tests/data/test_dicom/IMG0002.dcm
tests/data/test_dicom/IMG0003.dcm
tests/data/test_dicom/IMG0004.dcm
tests/data/test_dicom/IMG0005.dcm
tests/data/test_dicom/IMG0006.dcm
tests/data/test_dicom/IMG0007.dcm
tests/data/test_dicom/IMG0008.dcm
tests/data/test_dicom/IMG0009.dcm
tests/data/test_dicom/IMG0010.dcm
tests/data/test_dicom/IMG0011.dcm
tests/data/test_dicom/IMG0012.dcm
tests/data/test_dicom/IMG0013.dcm
tests/data/test_dicom/IMG0014.dcm
tests/data/test_dicom/IMG0015.dcm
tests/data/test_dicom/IMG0016.dcm
tests/data/test_dicom/IMG0017.dcm
tests/data/test_dicom/IMG0018.dcm
tests/data/test_dicom/IMG0019.dcm
tests/data/test_dicom/IMG0020.dcm
tests/data/test_dicom/IMG0021.dcm
tests/data/test_dicom/IMG0022.dcm
tests/data/test_dicom/IMG0023.dcm
tests/data/test_dicom/IMG0024.dcm
tests/data/test_dicom/IMG0025.dcm
tests/joint_space_analysis/__init__.py
tests/joint_space_analysis/test_bone_connectivity.py
tests/joint_space_analysis/test_jsw_morphometry.py
tests/laplace_hamming/test_laplace_hamming_filter.py
tests/segmentation/__init__.py
tests/segmentation/test_seg_gauss.py
tests/util/__init__.py
tests/util/test_file_converter.py
tests/util/test_file_reader.py
tests/util/test_hildebrand_thickness.py
tests/util/test_hrpqct_rescale.py
tests/util/test_itk_sitk_conversion.py
tests/util/test_scrub_vms_extension.py
tests/util/test_segmentation_evaluation.py
tests/util/test_vtk_sitk_conversion.py