├── .gitkeep ├── docker ├── jupyter │ ├── .gitkeep │ ├── .dockerignore │ └── environment.yml └── bidsapp │ ├── entrypoints │ ├── run_srr.sh │ └── run_srr_coverage.sh │ └── environment.yml ├── pymialsrtk ├── __init__.py ├── version ├── bids │ └── __init__.py ├── interfaces │ └── __init__.py ├── pipelines │ ├── __init__.py │ └── anatomical │ │ └── __init__.py ├── sphinxext │ ├── __init__.py │ └── gh.py ├── workflows │ └── __init__.py ├── cli │ └── __init__.py ├── utils.py ├── data │ └── Network_checkpoints │ │ ├── Network_checkpoints_localization │ │ ├── Unet.ckpt-88000.index │ │ ├── Unet.ckpt-88000.meta │ │ └── Unet.ckpt-88000.data-00000-of-00001 │ │ └── Network_checkpoints_segmentation │ │ ├── Unet.ckpt-20000.index │ │ ├── Unet.ckpt-20000.meta │ │ └── Unet.ckpt-20000.data-00000-of-00001 └── info.py ├── documentation ├── __init__.py ├── doxygen_html │ ├── search │ │ ├── classes_a.js │ │ ├── close.png │ │ ├── mag_sel.png │ │ ├── search_l.png │ │ ├── search_m.png │ │ ├── search_r.png │ │ ├── classes_8.js │ │ ├── functions_3.js │ │ ├── classes_10.js │ │ ├── classes_9.js │ │ ├── enums_1.js │ │ ├── functions_9.js │ │ ├── pages_0.js │ │ ├── enums_0.js │ │ ├── classes_e.js │ │ ├── classes_2.js │ │ ├── classes_3.js │ │ ├── typedefs_4.js │ │ ├── typedefs_7.js │ │ ├── all_8.js │ │ ├── classes_5.js │ │ ├── classes_f.js │ │ ├── classes_7.js │ │ ├── typedefs_0.js │ │ ├── all_b.js │ │ ├── classes_0.js │ │ ├── classes_d.js │ │ ├── functions_f.js │ │ ├── classes_6.js │ │ ├── functions_1.js │ │ ├── functions_8.js │ │ ├── nomatches.html │ │ ├── functions_5.js │ │ ├── classes_1.js │ │ ├── typedefs_2.js │ │ ├── typedefs_d.js │ │ ├── classes_b.js │ │ ├── typedefs_a.js │ │ ├── classes_c.js │ │ ├── all_3.js │ │ ├── functions_b.js │ │ ├── all_1.js │ │ ├── typedefs_3.js │ │ ├── typedefs_6.js │ │ ├── all_9.js │ │ ├── classes_4.js │ │ ├── all_0.html │ │ ├── all_1.html │ │ ├── all_10.html │ │ ├── all_11.html │ │ ├── all_12.html │ │ ├── all_13.html │ │ ├── all_14.html │ │ ├── all_2.html │ │ ├── all_3.html │ │ ├── all_4.html │ │ ├── all_5.html │ │ ├── all_6.html │ │ ├── all_7.html │ │ ├── all_8.html │ │ ├── all_9.html │ │ ├── all_a.html │ │ ├── all_b.html │ │ ├── all_c.html │ │ ├── all_d.html │ │ ├── all_e.html │ │ ├── all_f.html │ │ ├── enums_0.html │ │ ├── enums_1.html │ │ ├── pages_0.html │ │ ├── classes_0.html │ │ ├── classes_1.html │ │ ├── classes_10.html │ │ ├── classes_2.html │ │ ├── classes_3.html │ │ ├── classes_4.html │ │ ├── classes_5.html │ │ ├── classes_6.html │ │ ├── classes_7.html │ │ ├── classes_8.html │ │ ├── classes_9.html │ │ ├── classes_a.html │ │ ├── classes_b.html │ │ ├── classes_c.html │ │ ├── classes_d.html │ │ ├── classes_e.html │ │ ├── classes_f.html │ │ ├── functions_0.html │ │ ├── functions_1.html │ │ ├── functions_2.html │ │ ├── functions_3.html │ │ ├── functions_4.html │ │ ├── functions_5.html │ │ ├── functions_6.html │ │ ├── functions_7.html │ │ ├── functions_8.html │ │ ├── functions_9.html │ │ ├── functions_a.html │ │ ├── functions_b.html │ │ ├── functions_c.html │ │ ├── functions_d.html │ │ ├── functions_e.html │ │ ├── functions_f.html │ │ ├── typedefs_0.html │ │ ├── typedefs_1.html │ │ ├── typedefs_2.html │ │ ├── typedefs_3.html │ │ ├── typedefs_4.html │ │ ├── typedefs_5.html │ │ ├── typedefs_6.html │ │ ├── typedefs_7.html │ │ ├── typedefs_8.html │ │ ├── typedefs_9.html │ │ ├── typedefs_a.html │ │ ├── typedefs_b.html │ │ ├── typedefs_c.html │ │ ├── typedefs_d.html │ │ ├── variables_0.html │ │ ├── functions_10.html │ │ ├── functions_11.html │ │ ├── all_14.js │ │ ├── functions_a.js │ │ ├── functions_11.js │ │ ├── all_12.js │ │ ├── variables_0.js │ │ ├── all_5.js │ │ ├── functions_10.js │ │ ├── all_13.js │ │ ├── typedefs_1.js │ │ ├── typedefs_9.js │ │ └── typedefs_c.js │ ├── bc_s.png │ ├── bdwn.png │ ├── nav_f.png │ ├── nav_g.png │ ├── nav_h.png │ ├── open.png │ ├── tab_a.png │ ├── tab_b.png │ ├── tab_h.png │ ├── tab_s.png │ ├── closed.png │ ├── doxygen.png │ ├── ftv2cl.png │ ├── ftv2doc.png │ ├── ftv2mo.png │ ├── ftv2ns.png │ ├── sync_on.png │ ├── ftv2blank.png │ ├── ftv2link.png │ ├── ftv2mnode.png │ ├── ftv2node.png │ ├── ftv2pnode.png │ ├── sync_off.png │ ├── ftv2lastnode.png │ ├── ftv2splitbar.png │ ├── ftv2vertline.png │ ├── ftv2folderopen.png │ ├── ftv2mlastnode.png │ ├── ftv2plastnode.png │ ├── ftv2folderclosed.png │ ├── MIALSRTKlogo394x90.png │ ├── classbtk_1_1_p_s_f.png │ ├── classbtk_1_1_box_car_p_s_f.png │ ├── classbtk_1_1_gaussian_p_s_f.png │ ├── classmialsrtk_1_1_registration.png │ ├── classbtk_1_1_gradient_direction.png │ ├── classbtk_1_1_spherical_direction.png │ ├── classitk_1_1_f_f_t_pad_image_filter.png │ ├── classbtk_1_1_command_iteration_update.png │ ├── classbtk_1_1_command_progress_update.png │ ├── classmialsrtk_1_1_rigid_registration.png │ ├── classcrl_1_1_m_s_t_a_p_l_e_image_filter.png │ ├── classbtk_1_1_crop_image_using_mask_filter.png │ ├── classbtk_1_1_weighted_sum_of_images_filter.png │ ├── classmialsrtk_1_1_slice_by_slice_transform.png │ ├── classitk_1_1_b_spline_resample_image_function.png │ ├── classmialsrtk_1_1_oriented_spatial_function.png │ ├── classmialsrtk_1_1_image_intersection_calculator.png │ ├── classmialsrtk_1_1_slice_by_slice_transform_base.png │ ├── classmialsrtk_1_1_versor_slice_by_slice_transform.png │ ├── classbtk_1_1_resample_images_to_biggest_image_filter.png │ ├── classmialsrtk_1_1_resample_image_by_injection_filter.png │ ├── classmialsrtk_1_1_slice_by_slice_rigid_registration.png │ ├── classmialsrtk_1_1_b_spline_interpolate_image_function.png │ ├── classmialsrtk_1_1_low_to_high_image_resolution_method.png │ ├── classbtk_1_1_linear_interpolate_image_function_with_weights.png │ ├── classmialsrtk_fetal_brain_extraction_g_u_i_1_1_main_window.png │ ├── classitk_1_1_compute_normalized_cross_correlation_image_filter.png │ ├── classmialsrtk_fetal_brain_extraction_g_u_i_1_1_ui___main_window.png │ ├── classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.png │ ├── classmialsrtk_1_1_super_resolution_rigid_image_filter_with_implicit_gradient_descent.png │ └── tabs.css ├── images │ ├── html_report_1.png │ ├── html_report_2.png │ ├── html_report_3.png │ ├── mialsrtk-logo.png │ ├── nipype_wf_graph.png │ ├── nipype_node_report.png │ └── nipype_wf_derivatives.png ├── api_utils.rst ├── api_postprocess.rst ├── api_preprocess.rst ├── api_reconstruction.rst ├── requirements.txt ├── api_pipelines.rst ├── api_commandlineinterface.rst ├── mainpage.md ├── api_workflows.rst ├── citing.rst └── LICENSE.rst ├── contributors.txt ├── data ├── code │ ├── batch_list.txt │ ├── sub-01_ses-01_scans.txt │ ├── sub-01_ses-02_scans.txt │ ├── participants_params.json │ ├── create_dataset_description_json.sh │ └── create_scan_preproc_json.sh ├── .bidsignore ├── CHANGES ├── participants.tsv ├── sub-01 │ └── anat │ │ ├── sub-01_run-1_T2w.nii.gz │ │ ├── sub-01_run-2_T2w.nii.gz │ │ ├── sub-01_run-3_T2w.nii.gz │ │ ├── sub-01_run-4_T2w.nii.gz │ │ ├── sub-01_run-5_T2w.nii.gz │ │ ├── sub-01_run-6_T2w.nii.gz │ │ ├── sub-01_run-1_T2w.json │ │ ├── sub-01_run-2_T2w.json │ │ └── sub-01_run-5_T2w.json ├── dataset_description.json ├── derivatives │ └── manual_masks │ │ ├── sub-01 │ │ └── anat │ │ │ ├── sub-01_run-1_T2w_desc-brain_mask.json │ │ │ ├── sub-01_run-2_T2w_desc-brain_mask.json │ │ │ ├── sub-01_run-3_T2w_desc-brain_mask.json │ │ │ ├── sub-01_run-4_T2w_desc-brain_mask.json │ │ │ ├── sub-01_run-5_T2w_desc-brain_mask.json │ │ │ ├── sub-01_run-6_T2w_desc-brain_mask.json │ │ │ ├── sub-01_run-1_T2w_desc-brain_mask.nii.gz │ │ │ ├── sub-01_run-2_T2w_desc-brain_mask.nii.gz │ │ │ ├── sub-01_run-3_T2w_desc-brain_mask.nii.gz │ │ │ ├── sub-01_run-4_T2w_desc-brain_mask.nii.gz │ │ │ ├── sub-01_run-5_T2w_desc-brain_mask.nii.gz │ │ │ └── sub-01_run-6_T2w_desc-brain_mask.nii.gz │ │ └── dataset_description.json ├── participants.json └── README ├── src ├── Code │ └── Transformations │ │ └── mialsrtkSliceBySliceTransformBase.txx ├── Resources │ ├── resources.qrc │ ├── MIALlogo220x60.png │ ├── MIALlogo330x90.png │ └── MIALSRTKlogo394x90.png ├── Denoising │ └── CMakeLists.txt ├── cmake_uninstall.cmake.in ├── BrainLocalizationExtraction │ └── CMakeLists.txt ├── SuperResolution │ └── CMakeLists.txt ├── Tools │ └── CMakeLists.txt └── Evaluation │ └── CMakeLists.txt ├── .gitattributes ├── notebooks └── data │ ├── graph.png │ ├── sub-01_rec-SR_id-1_T2w.png │ ├── sub-01_rec-SR_id-1_T2w.nii.gz │ ├── sub-01_rec-SR_id-1_desc-motion_stats.png │ └── sub-01_rec-SR_id-1_T2w.json ├── scripts ├── build_sphinx_docs.sh ├── test_bidsapp_docker_wrapper.sh ├── test_bidsapp.sh ├── build_bidsapp.sh └── build_jupyter.sh ├── .dockerignore ├── get_version.py ├── examples └── run_docker_jupyter.sh ├── .readthedocs.yml ├── .travis.yml ├── .gitignore ├── pep8speaks.yml └── LICENSE.txt /.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docker/jupyter/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymialsrtk/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymialsrtk/version: -------------------------------------------------------------------------------- 1 | dev -------------------------------------------------------------------------------- /documentation/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymialsrtk/bids/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymialsrtk/interfaces/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymialsrtk/pipelines/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymialsrtk/sphinxext/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /pymialsrtk/workflows/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /contributors.txt: -------------------------------------------------------------------------------- 1 | Sébastien Tourbier 2 | -------------------------------------------------------------------------------- /data/code/batch_list.txt: -------------------------------------------------------------------------------- 1 | sub-01 ses-01 0.75 0.01 2 | -------------------------------------------------------------------------------- /data/.bidsignore: -------------------------------------------------------------------------------- 1 | { 2 | "ignoredFiles": ["*/tmp/**"] 3 | } -------------------------------------------------------------------------------- /data/CHANGES: -------------------------------------------------------------------------------- 1 | 1.0.0 2019-05-10 2 | 3 | - initial release -------------------------------------------------------------------------------- /src/Code/Transformations/mialsrtkSliceBySliceTransformBase.txx: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | Unet.ckpt-* filter=lfs diff=lfs merge=lfs -text 2 | -------------------------------------------------------------------------------- /data/participants.tsv: -------------------------------------------------------------------------------- 1 | participant_id sex age 2 | sub-01 n/a n/a 3 | 4 | -------------------------------------------------------------------------------- /pymialsrtk/cli/__init__.py: -------------------------------------------------------------------------------- 1 | """This module defines commandline scripts.""" -------------------------------------------------------------------------------- /pymialsrtk/utils.py: -------------------------------------------------------------------------------- 1 | """ 2 | Absolute path to the exectuable files 3 | """ 4 | EXEC_PATH = '/usr/local/bin/' 5 | -------------------------------------------------------------------------------- /src/Resources/resources.qrc: -------------------------------------------------------------------------------- 1 | 2 | 3 | ../Resources/MIALlogo220x60.png 4 | 5 | 6 | -------------------------------------------------------------------------------- /data/code/sub-01_ses-01_scans.txt: -------------------------------------------------------------------------------- 1 | run-1 axial 2 | run-3 coronal 3 | run-5 sagittal 4 | run-2 axial 5 | run-4 coronal 6 | run-6 sagittal 7 | -------------------------------------------------------------------------------- /data/code/sub-01_ses-02_scans.txt: -------------------------------------------------------------------------------- 1 | run-1 axial 2 | run-2 coronal 3 | run-3 sagittal 4 | run-4 coronal 5 | run-5 sagittal 6 | run-6 sagittal 7 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_a.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['psf',['PSF',['../classbtk_1_1_p_s_f.html',1,'btk']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /notebooks/data/graph.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/HEAD/notebooks/data/graph.png -------------------------------------------------------------------------------- /pymialsrtk/pipelines/anatomical/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Init file 3 | """ 4 | from .srr import SRReconPipeline 5 | from .preprocessing import PreprocessingPipeline 6 | -------------------------------------------------------------------------------- /src/Resources/MIALlogo220x60.png: -------------------------------------------------------------------------------- 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/data/participants.json: -------------------------------------------------------------------------------- 1 | { 2 | "age": { 3 | "Description": "Gestational age", 4 | "Units": "weeks" 5 | }, 6 | 7 | "sex": { 8 | "Description": "sex of the fetus", 9 | "Levels": { 10 | "m": "male", 11 | "f": "female", 12 | "na": "not attributed" 13 | } 14 | } 15 | } 16 | 17 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/all_b.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['neighborhooditeratortype',['NeighborhoodIteratorType',['../classmialsrtk_1_1_resample_image_by_injection_filter.html#a46770386c6672dae32f71d66bf3ab4ef',1,'mialsrtk::ResampleImageByInjectionFilter']]], 4 | ['nlm',['NLM',['../class_n_l_m.html',1,'']]], 5 | ['nlmtool',['NLMTool',['../classbtk_1_1_n_l_m_tool.html',1,'btk']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /docker/jupyter/.dockerignore: -------------------------------------------------------------------------------- 1 | *.pklz 2 | *.pyc 3 | *.npz 4 | *.xdebug_tkmedit 5 | *.mp4 6 | atom-config.txt 7 | 8 | .DS_Store? 9 | .DS_Store 10 | ehthumbs.db 11 | Icon? 12 | Thumbs.db 13 | 14 | docs 15 | docs/* 16 | 17 | docker 18 | docker/* 19 | 20 | debian 21 | debian/* 22 | 23 | dist 24 | dist/* 25 | 26 | build 27 | build/* 28 | 29 | _build 30 | _static 31 | _templates 32 | 33 | *.ipynb_checkpoints 34 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_0.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['boxcarpsf',['BoxCarPSF',['../classbtk_1_1_box_car_p_s_f.html',1,'btk']]], 4 | ['bsplineinterpolateimagefunction',['BSplineInterpolateImageFunction',['../classmialsrtk_1_1_b_spline_interpolate_image_function.html',1,'mialsrtk']]], 5 | ['bsplineresampleimagefunction',['BSplineResampleImageFunction',['../classitk_1_1_b_spline_resample_image_function.html',1,'itk']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /scripts/test_bidsapp_docker_wrapper.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | SCRIPTSDIR=$(cd "$(dirname "$0")"; pwd) 3 | BASEDIR="$(dirname "$SCRIPTSDIR")" 4 | 5 | mialsuperresolutiontoolkit_docker \ 6 | "$BASEDIR/data" \ 7 | "$BASEDIR/data/derivatives" \ 8 | participant --participant_label 01 \ 9 | --param_file "$BASEDIR/data/code/participants_params.json" \ 10 | --nipype_nb_of_cores 1 \ 11 | --openmp_nb_of_cores 1 \ 12 | --track_carbon_footprint 13 | -------------------------------------------------------------------------------- /documentation/api_pipelines.rst: -------------------------------------------------------------------------------- 1 | .. _apidoc_pipelines: 2 | 3 | ****************** 4 | Pipelines module 5 | ****************** 6 | 7 | .. automodule:: pymialsrtk.pipelines.anatomical.abstract 8 | :members: 9 | :show-inheritance: 10 | 11 | .. automodule:: pymialsrtk.pipelines.anatomical.preprocessing 12 | :members: 13 | :show-inheritance: 14 | 15 | .. automodule:: pymialsrtk.pipelines.anatomical.srr 16 | :members: 17 | :show-inheritance: 18 | -------------------------------------------------------------------------------- /documentation/api_commandlineinterface.rst: -------------------------------------------------------------------------------- 1 | .. _apidoc_cli: 2 | 3 | ************************************ 4 | Command-line interface (CLI) module 5 | ************************************ 6 | 7 | .. automodule:: pymialsrtk.cli.mialsuperresolutiontoolkit_docker 8 | :members: 9 | :undoc-members: 10 | :show-inheritance: 11 | 12 | .. automodule:: pymialsrtk.cli.mialsuperresolutiontoolkit_singularity 13 | :members: 14 | :undoc-members: 15 | :show-inheritance: 16 | -------------------------------------------------------------------------------- /docker/bidsapp/entrypoints/run_srr_coverage.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | echo "User: $(id -un "$USER")" && echo "Group: $(id -gn "$USER")" && \ 3 | export && \ 4 | echo "SHELL: $SHELL" && \ 5 | echo "PATH: $PATH" && \ 6 | xvfb-run -a coverage run --source=pymialsrtk \ 7 | /app/run.py "$@" \ 8 | |& tee /bids_dir/code/log.txt && \ 9 | coverage html -d /bids_dir/code/coverage_html && \ 10 | coverage xml -o /bids_dir/code/coverage.xml && \ 11 | coverage json -o /bids_dir/code/coverage.json 12 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_d.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['threadstruct',['ThreadStruct',['../structitk_1_1_compute_normalized_cross_correlation_image_filter_1_1_thread_struct.html',1,'itk::ComputeNormalizedCrossCorrelationImageFilter']]], 4 | ['totalvariationcostfunctionwithimplicitgradientdescent',['TotalVariationCostFunctionWithImplicitGradientDescent',['../classmialsrtk_1_1_total_variation_cost_function_with_implicit_gradient_descent.html',1,'mialsrtk']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/functions_f.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['verifyinputinformation',['VerifyInputInformation',['../classmialsrtk_1_1_resample_image_by_injection_filter.html#a90f9049d6064a0fa4d6e362f6fd56fa8',1,'mialsrtk::ResampleImageByInjectionFilter']]], 4 | ['versorslicebyslicetransform',['VersorSliceBySliceTransform',['../classmialsrtk_1_1_versor_slice_by_slice_transform.html#ab30fbb64916b6c547dfaeb1023acf562',1,'mialsrtk::VersorSliceBySliceTransform']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /data/README: -------------------------------------------------------------------------------- 1 | This sample BIDS dataset contains a set of three orthogonal MRI 2 | with anisotropic resolution (1x1x2mm^3) of the fetal brain of subject "sub-01" 3 | acquired with a fast multi-slice sequence. 4 | 5 | Manually drawn brain masks can be found in derivatives/manual_masks/sub-01/anat folder 6 | 7 | The text file listing the scans used by the supperresolution_pipeline.sh script 8 | can be found in code/ as sub-01_ses-01_scans.txt 9 | 10 | - Sebastien Tourbier (May 10, 2019) -------------------------------------------------------------------------------- /.dockerignore: -------------------------------------------------------------------------------- 1 | *.pklz 2 | *.pyc 3 | *.npz 4 | *.xdebug_tkmedit 5 | *.mp4 6 | atom-config.txt 7 | 8 | .DS_Store? 9 | .DS_Store 10 | ehthumbs.db 11 | Icon? 12 | Thumbs.db 13 | 14 | documentation 15 | documentation/* 16 | 17 | data 18 | data/* 19 | 20 | debian 21 | debian/* 22 | 23 | dist 24 | dist/* 25 | 26 | build 27 | build/* 28 | 29 | _build 30 | _static 31 | _templates 32 | 33 | notebooks 34 | notebooks/* 35 | *.ipynb_checkpoints 36 | 37 | examples 38 | examples/* 39 | 40 | scripts 41 | scripts/* 42 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_6.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['linearinterpolateimagefunction',['LinearInterpolateImageFunction',['../class_linear_interpolate_image_function.html',1,'']]], 4 | ['linearinterpolateimagefunctionwithweights',['LinearInterpolateImageFunctionWithWeights',['../classbtk_1_1_linear_interpolate_image_function_with_weights.html',1,'btk']]], 5 | ['lowtohighimageresolutionmethod',['LowToHighImageResolutionMethod',['../classmialsrtk_1_1_low_to_high_image_resolution_method.html',1,'mialsrtk']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/functions_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['boxcarpsf',['BoxCarPSF',['../classbtk_1_1_box_car_p_s_f.html#a00ed02951517bc5686c86708f468f8bb',1,'btk::BoxCarPSF']]], 4 | ['bsplineinterpolateimagefunction',['BSplineInterpolateImageFunction',['../classmialsrtk_1_1_b_spline_interpolate_image_function.html#af125b75194ee8144f768327a8f247d3d',1,'mialsrtk::BSplineInterpolateImageFunction']]], 5 | ['btkgetmacro',['btkGetMacro',['../classbtk_1_1_p_s_f.html#ae0b1e4f95881ff5c5705f0a60ab2e479',1,'btk::PSF']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /notebooks/data/sub-01_rec-SR_id-1_T2w.json: -------------------------------------------------------------------------------- 1 | { 2 | "Description": "Isotropic high-resolution image reconstructed using the Total-Variation Super-Resolution algorithm provided by MIALSRTK", 3 | "Input sources run order": [ 4 | 6, 5 | 3, 6 | 1 7 | ], 8 | "CustomMetaData": { 9 | "Number of scans used": "3", 10 | "Masks used": "Automatic", 11 | "TV regularization weight lambda": 0.75, 12 | "Optimization time step": 0.01, 13 | "Primal/dual loops": 10 14 | } 15 | } -------------------------------------------------------------------------------- /documentation/doxygen_html/search/functions_8.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | 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9 |
No Matches
10 |
11 | 12 | 13 | -------------------------------------------------------------------------------- /get_version.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- coding: utf-8 -*- 3 | # @Author: sebastientourbier 4 | # @Date: 2019-09-06 13:39:38 5 | 6 | """Standalone script that print the version of MIALSRTK installed.""" 7 | 8 | import sys 9 | import os.path as op 10 | 11 | 12 | def main(): 13 | """Main function that read and print the version of MIALSRTK installed.""" 14 | 15 | sys.path.insert(0, op.abspath('.')) 16 | from pymialsrtk.info import __version__ 17 | print(__version__) 18 | 19 | 20 | if __name__ == '__main__': 21 | main() 22 | -------------------------------------------------------------------------------- /data/code/create_dataset_description_json.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # 3 | # Usage: 4 | # sh create_dataset_description_json output.json v1.1.0 5 | # 6 | # Author: Sebastien Tourbier 7 | # 8 | ################################################################### 9 | 10 | OUTPUT_JSON=$1 11 | 12 | ( 13 | cat < $OUTPUT_JSON 24 | -------------------------------------------------------------------------------- /examples/run_docker_jupyter.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/sh 2 | 3 | mialsrtk_dir="/home/hkebiri/mialsuperresolutiontoolkit" 4 | data_dir="/home/hkebiri/mialsuperresolutiontoolkit/data" 5 | 6 | port=8888 7 | 8 | version=v2.0.0 9 | 10 | cmd="docker run --rm" 11 | cmd="$cmd -v "${mialsrtk_dir}/notebooks":/app/notebooks" 12 | cmd="$cmd -v "${mialsrtk_dir}":/app/mialsuperresolutiontoolkit" 13 | cmd="$cmd -v "${data_dir}":/fetaldata" 14 | cmd="$cmd -p ${port}:${port}" 15 | cmd="$cmd -t sebastientourbier/mialsuperresolutiontoolkit-jupyter:${version}" 16 | 17 | eval $cmd 18 | 19 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/functions_5.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['fileexist',['FileExist',['../classbtk_1_1_file_helper.html#ad0566ddefe9ac01a670506e4f0fe967a',1,'btk::FileHelper']]], 4 | ['fileexistprintit',['FileExistPrintIt',['../classbtk_1_1_file_helper.html#a278a347759a7b577b23b4e011bc86e89',1,'btk::FileHelper']]], 5 | ['filesexist',['FilesExist',['../classbtk_1_1_file_helper.html#aa830b729d93d6889b0fec487a49530a6',1,'btk::FileHelper']]], 6 | ['filesexistprintit',['FilesExistPrintIt',['../classbtk_1_1_file_helper.html#a3257638607e19d6532247279f7cab017',1,'btk::FileHelper']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /data/code/create_scan_preproc_json.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # 3 | # Usage: 4 | # sh create_scan_preproc_json output.json source.nii.gz 5 | # 6 | # Author: Sebastien Tourbier 7 | # 8 | ################################################################### 9 | 10 | OUTPUT_JSON=$1 11 | 12 | ( 13 | cat < $OUTPUT_JSON 26 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['commanditerationupdate',['CommandIterationUpdate',['../classbtk_1_1_command_iteration_update.html',1,'btk']]], 4 | ['commandprogressupdate',['CommandProgressUpdate',['../classbtk_1_1_command_progress_update.html',1,'btk']]], 5 | ['computenormalizedcrosscorrelationimagefilter',['ComputeNormalizedCrossCorrelationImageFilter',['../classitk_1_1_compute_normalized_cross_correlation_image_filter.html',1,'itk']]], 6 | ['cropimageusingmaskfilter',['CropImageUsingMaskFilter',['../classbtk_1_1_crop_image_using_mask_filter.html',1,'btk']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /scripts/test_bidsapp.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | SCRIPTSDIR=$(cd "$(dirname "$0")"; pwd) 3 | BASEDIR="$(dirname "$SCRIPTSDIR")" 4 | 5 | # DOCKER_IMAGE="docker.io/sebastientourbier/mialsuperresolutiontoolkit-bidsapp:v2.0.3" 6 | DOCKER_IMAGE="sebastientourbier/mialsuperresolutiontoolkit-bidsapp:v2.0.3" 7 | 8 | docker run -it --rm -u $(id -u):$(id -g) \ 9 | -v "$BASEDIR/data":/bids_dir \ 10 | -v "$BASEDIR/data/derivatives":/output_dir \ 11 | "$DOCKER_IMAGE" \ 12 | /bids_dir /output_dir participant --participant_label 01 \ 13 | --param_file /bids_dir/code/participants_params.json \ 14 | --nipype_nb_of_cores 2 \ 15 | --openmp_nb_of_cores 1 16 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/typedefs_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['directiontype',['DirectionType',['../classbtk_1_1_p_s_f.html#a78f2e63c1f8ef76a04ad91ff47fb128b',1,'btk::PSF::DirectionType()'],['../classmialsrtk_1_1_oriented_spatial_function.html#ae18fbc59658dd52d93d25c36321831ff',1,'mialsrtk::OrientedSpatialFunction::DirectionType()'],['../classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.html#ad57e5f27e5d45180106c22ff240fef9e',1,'mialsrtk::RobustSuperResolutionRigidImageFilterWithGMM::DirectionType()'],['../classmialsrtk_1_1_super_resolution_rigid_image_filter_with_implicit_gradient_descent.html#a306655b7261df32b85319075f2adaa11',1,'mialsrtk::SuperResolutionRigidImageFilterWithImplicitGradientDescent::DirectionType()']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/typedefs_d.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['vectorimageiteratortype',['VectorImageIteratorType',['../classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.html#acfc6c58be7b7cb7df3bf0b92ab164b9e',1,'mialsrtk::RobustSuperResolutionRigidImageFilterWithGMM']]], 4 | ['vnlvectortype',['VnlVectorType',['../classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.html#a5c82ed951159d9bd3d999a34947374cb',1,'mialsrtk::RobustSuperResolutionRigidImageFilterWithGMM::VnlVectorType()'],['../classmialsrtk_1_1_super_resolution_rigid_image_filter_with_implicit_gradient_descent.html#ab731855ff25c282a8d87caf449641ffb',1,'mialsrtk::SuperResolutionRigidImageFilterWithImplicitGradientDescent::VnlVectorType()']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_b.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['registration',['Registration',['../classmialsrtk_1_1_registration.html',1,'mialsrtk']]], 4 | ['resampleimagebyinjectionfilter',['ResampleImageByInjectionFilter',['../classmialsrtk_1_1_resample_image_by_injection_filter.html',1,'mialsrtk']]], 5 | ['resampleimagestobiggestimagefilter',['ResampleImagesToBiggestImageFilter',['../classbtk_1_1_resample_images_to_biggest_image_filter.html',1,'btk']]], 6 | ['rigidregistration',['RigidRegistration',['../classmialsrtk_1_1_rigid_registration.html',1,'mialsrtk']]], 7 | ['robustsuperresolutionrigidimagefilterwithgmm',['RobustSuperResolutionRigidImageFilterWithGMM',['../classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.html',1,'mialsrtk']]] 8 | ]; 9 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/typedefs_a.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['realtype',['RealType',['../classbtk_1_1_linear_interpolate_image_function_with_weights.html#a0fbb0e96bd2d03dcc252a12a9352c17a',1,'btk::LinearInterpolateImageFunctionWithWeights']]], 4 | ['registrationbase',['RegistrationBase',['../classmialsrtk_1_1_low_to_high_image_resolution_method.html#a2a2c9c502963ec8184acb28f920bb979',1,'mialsrtk::LowToHighImageResolutionMethod']]], 5 | ['registrationtype',['RegistrationType',['../classmialsrtk_1_1_slice_by_slice_rigid_registration.html#a418e92e789099c635f5a8710c3a1fa3b',1,'mialsrtk::SliceBySliceRigidRegistration']]], 6 | ['rigidtransformtype',['RigidTransformType',['../classmialsrtk_1_1_rigid_registration.html#adc620af1697f2544c96317269e1cc7b0',1,'mialsrtk::RigidRegistration']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_c.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['slicebyslicerigidregistration',['SliceBySliceRigidRegistration',['../classmialsrtk_1_1_slice_by_slice_rigid_registration.html',1,'mialsrtk']]], 4 | ['slicebyslicetransform',['SliceBySliceTransform',['../classmialsrtk_1_1_slice_by_slice_transform.html',1,'mialsrtk']]], 5 | ['slicebyslicetransformbase',['SliceBySliceTransformBase',['../classmialsrtk_1_1_slice_by_slice_transform_base.html',1,'mialsrtk']]], 6 | ['sphericaldirection',['SphericalDirection',['../classbtk_1_1_spherical_direction.html',1,'btk']]], 7 | ['superresolutionrigidimagefilterwithimplicitgradientdescent',['SuperResolutionRigidImageFilterWithImplicitGradientDescent',['../classmialsrtk_1_1_super_resolution_rigid_image_filter_with_implicit_gradient_descent.html',1,'mialsrtk']]] 8 | ]; 9 | -------------------------------------------------------------------------------- /documentation/mainpage.md: -------------------------------------------------------------------------------- 1 | # # 2 | # WELCOME TO MIALSRTK SOURCE CODE DOCUMENTATION # 3 | 4 | The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ image processing tools necessary to perform motion-robust super-resolution fetal MRI reconstruction. It uses the CMake build system and depends on the open-source image processing Insight ToolKit (ITK) library, the command line parser TCLAP library and OpenMP for multi-threading. 5 | 6 | The USAGE message of each tool can be obained using either the -h or --help flag. 7 | 8 | 9 | 10 | # Contact # 11 | 12 | * Sébastien Tourbier - sebastien(dot)tourbier1(at)gmail(dot)com 13 | 14 | 15 | # # 16 | 17 | --- 18 | 19 | Copyright © 2016-2017 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland 20 | 21 | 22 | 23 | -------------------------------------------------------------------------------- /documentation/api_workflows.rst: -------------------------------------------------------------------------------- 1 | .. _apidoc_workflows: 2 | 3 | ****************** 4 | Workflows module 5 | ****************** 6 | 7 | .. automodule:: pymialsrtk.workflows.input_stage 8 | :members: 9 | :show-inheritance: 10 | 11 | .. automodule:: pymialsrtk.workflows.preproc_stage 12 | :members: 13 | :show-inheritance: 14 | 15 | .. automodule:: pymialsrtk.workflows.registration_stage 16 | :members: 17 | :show-inheritance: 18 | 19 | .. automodule:: pymialsrtk.workflows.recon_stage 20 | :members: 21 | :show-inheritance: 22 | 23 | .. automodule:: pymialsrtk.workflows.recon_labelmap_stage 24 | :members: 25 | :show-inheritance: 26 | 27 | .. automodule:: pymialsrtk.workflows.srr_assessment_stage 28 | :members: 29 | :show-inheritance: 30 | 31 | .. automodule:: pymialsrtk.workflows.output_stage 32 | :members: 33 | :show-inheritance: 34 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/all_3.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['deepcopy',['DeepCopy',['../classbtk_1_1_image_helper.html#a9f2d9b30bf467da162161e802fa323a9',1,'btk::ImageHelper']]], 4 | ['directiontype',['DirectionType',['../classbtk_1_1_p_s_f.html#a78f2e63c1f8ef76a04ad91ff47fb128b',1,'btk::PSF::DirectionType()'],['../classmialsrtk_1_1_oriented_spatial_function.html#ae18fbc59658dd52d93d25c36321831ff',1,'mialsrtk::OrientedSpatialFunction::DirectionType()'],['../classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.html#ad57e5f27e5d45180106c22ff240fef9e',1,'mialsrtk::RobustSuperResolutionRigidImageFilterWithGMM::DirectionType()'],['../classmialsrtk_1_1_super_resolution_rigid_image_filter_with_implicit_gradient_descent.html#a306655b7261df32b85319075f2adaa11',1,'mialsrtk::SuperResolutionRigidImageFilterWithImplicitGradientDescent::DirectionType()']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | # Required 6 | version: 2 7 | 8 | # Build documentation in the docs/ directory with Sphinx 9 | sphinx: 10 | configuration: documentation/conf.py 11 | 12 | # Build documentation with MkDocs 13 | #mkdocs: 14 | # configuration: mkdocs.yml 15 | 16 | # Optionally build your docs in additional formats such as PDF 17 | formats: 18 | - htmlzip 19 | - pdf 20 | 21 | # # Install the pymialsrtk conda environment with all dependencies required to build the doc 22 | # conda: 23 | # environment: docker/bidsapp/environment.yml 24 | 25 | # Optionally set the version of Python and requirements required to build your docs 26 | python: 27 | version: 3.7 28 | install: 29 | - requirements: documentation/requirements.txt 30 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/functions_b.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['readconstimage',['ReadConstImage',['../classbtk_1_1_image_helper.html#ade5e57f6702891e65512d3a99d204b6a',1,'btk::ImageHelper']]], 4 | ['readimage',['ReadImage',['../classbtk_1_1_image_helper.html#ae6b9563f6aed71d1857cafd0bc5f04f8',1,'btk::ImageHelper::ReadImage(const std::string &fileName)'],['../classbtk_1_1_image_helper.html#aae9e25a64d47457635441b7a3342d6bc',1,'btk::ImageHelper::ReadImage(std::vector< std::string > &fileNames)']]], 5 | ['readorcreateimage',['ReadOrCreateImage',['../classbtk_1_1_image_helper.html#a1a743c17602caa57f8fa60c1ae681893',1,'btk::ImageHelper']]], 6 | ['resampleimagestobiggestimagefilter',['ResampleImagesToBiggestImageFilter',['../classbtk_1_1_resample_images_to_biggest_image_filter.html#a54ab58f62176724095f026d244109804',1,'btk::ResampleImagesToBiggestImageFilter']]] 7 | ]; 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7 | -------------------------------------------------------------------------------- /docker/bidsapp/environment.yml: -------------------------------------------------------------------------------- 1 | name: base 2 | 3 | channels: 4 | - conda-forge 5 | - defaults 6 | - anaconda 7 | - aramislab 8 | 9 | dependencies: 10 | - python=3.7.10 11 | - pip=21.0.1 12 | - pandas=1.1.5 13 | - nipype=1.8.4 14 | - nilearn=0.8.0 15 | - pydotplus=2.0.2 16 | - pandoc=2.14.2 17 | - seaborn=0.11.2 18 | - matplotlib=3.4 19 | - tensorflow==1.13.1 20 | - scikit-learn=0.21.3 21 | - scikit-image=0.16.2 22 | - ants=2.2.0 23 | 24 | - pip: 25 | - coverage==5.1 26 | - duecredit==0.8.0 27 | - graphviz 28 | - tflearn==0.3.2 29 | - MedPy==0.4.0 30 | - opencv-python==4.1.0.25 31 | - sphinx==1.8.5 32 | - sphinx_rtd_theme==0.4.3 33 | - sphinx-argparse==0.2.5 34 | - nbsphinx==0.7.1 35 | - sphinxcontrib-apidoc==0.3.0 36 | - sphinxcontrib-napoleon==0.7 37 | - recommonmark==0.5.0 38 | - etelemetry==0.3.0 39 | - networkx==2.6.3 40 | - simpleITK==2.0.2 41 | - nsol==0.1.14 42 | - nipy==0.5.0 43 | - transforms3d==0.3.1 44 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/all_9.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['linearinterpolateimagefunction',['LinearInterpolateImageFunction',['../class_linear_interpolate_image_function.html',1,'']]], 4 | ['linearinterpolateimagefunctionwithweights',['LinearInterpolateImageFunctionWithWeights',['../classbtk_1_1_linear_interpolate_image_function_with_weights.html',1,'btk']]], 5 | ['lineartoabsoluteindex',['LinearToAbsoluteIndex',['../classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.html#a2574bfaac5374270fefac1bf8fa44efd',1,'mialsrtk::RobustSuperResolutionRigidImageFilterWithGMM::LinearToAbsoluteIndex()'],['../classmialsrtk_1_1_super_resolution_rigid_image_filter_with_implicit_gradient_descent.html#a24e55fbc9bb4193f53cfdfbeac9124f4',1,'mialsrtk::SuperResolutionRigidImageFilterWithImplicitGradientDescent::LinearToAbsoluteIndex()']]], 6 | ['lowtohighimageresolutionmethod',['LowToHighImageResolutionMethod',['../classmialsrtk_1_1_low_to_high_image_resolution_method.html',1,'mialsrtk']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_4.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['imagehelper',['ImageHelper',['../classbtk_1_1_image_helper.html',1,'btk']]], 4 | ['imageintersectioncalculator',['ImageIntersectionCalculator',['../classmialsrtk_1_1_image_intersection_calculator.html',1,'mialsrtk']]], 5 | ['imageregistrationfilter',['ImageRegistrationFilter',['../classmialsrtk_1_1_image_registration_filter.html',1,'mialsrtk']]], 6 | ['img_5fsize',['img_size',['../structimg__size.html',1,'']]], 7 | ['img_5fsize',['img_size',['../structmialsrtk_1_1_total_variation_cost_function_with_implicit_gradient_descent_1_1img__size.html',1,'mialsrtk::TotalVariationCostFunctionWithImplicitGradientDescent']]], 8 | ['img_5fsize',['img_size',['../structmialsrtk_1_1_joint_robust_t_v_g_m_m_cost_function_with_implicit_gradient_descent_1_1img__size.html',1,'mialsrtk::JointRobustTVGMMCostFunctionWithImplicitGradientDescent']]], 9 | ['ioimagehelper',['IOImageHelper',['../classbtk_1_1_i_o_image_helper.html',1,'btk']]] 10 | ]; 11 | -------------------------------------------------------------------------------- /scripts/build_bidsapp.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | SCRIPTSDIR=$(cd "$(dirname "$0")"; pwd) 3 | BASEDIR="$(dirname "$SCRIPTSDIR")" 4 | cd "$BASEDIR" 5 | 6 | CMP_BUILD_DATE="$(date -u +\"%Y-%m-%dT%H:%M:%SZ\")" 7 | echo "$CMP_BUILD_DATE" 8 | 9 | VERSION="v$(python get_version.py)" 10 | echo "$VERSION" 11 | 12 | VCS_REF="$(git rev-parse --verify HEAD)" 13 | echo "$VCS_REF" 14 | 15 | MAIN_DOCKER="sebastientourbier/mialsuperresolutiontoolkit-ubuntu14.04:${VERSION}" 16 | echo "$MAIN_DOCKER" 17 | 18 | docker build --rm --build-arg BUILD_DATE="$CMP_BUILD_DATE" \ 19 | --build-arg VCS_REF="$VCS_REF" \ 20 | --build-arg VERSION="$VERSION" \ 21 | -t "${MAIN_DOCKER}" "$BASEDIR" 22 | 23 | docker build --rm --build-arg BUILD_DATE="$CMP_BUILD_DATE" \ 24 | --build-arg VERSION="$VERSION" \ 25 | --build-arg VCS_REF="$VCS_REF" \ 26 | --build-arg MAIN_DOCKER="$MAIN_DOCKER" \ 27 | -t sebastientourbier/mialsuperresolutiontoolkit-bidsapp:"${VERSION}" "$BASEDIR/docker/bidsapp" 28 | 29 | -------------------------------------------------------------------------------- /src/Denoising/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(Denoising) 2 | INCLUDE_REGULAR_EXPRESSION("^.*$") 3 | 4 | INCLUDE_DIRECTORIES(${TCLAP_DIRECTORY}) 5 | INCLUDE_DIRECTORIES(${ANN_INCLUDE_DIR}) 6 | INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/BTK) 7 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Transformations) 8 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Maths) 9 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Registration) 10 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Maths) 11 | 12 | ADD_EXECUTABLE(btkNLMDenoising btkNLMDenoising.cxx) 13 | TARGET_LINK_LIBRARIES(btkNLMDenoising ${ITK_LIBRARIES}) 14 | 15 | ADD_EXECUTABLE(mialsrtkTVDenoising mialsrtkTVDenoising.cxx) 16 | TARGET_LINK_LIBRARIES(mialsrtkTVDenoising ${ITK_LIBRARIES}) 17 | 18 | ADD_EXECUTABLE(mialsrtkGaussianDenoising mialsrtkGaussianDenoising.cxx) 19 | TARGET_LINK_LIBRARIES(mialsrtkGaussianDenoising ${ITK_LIBRARIES}) 20 | 21 | INSTALL(TARGETS 22 | btkNLMDenoising 23 | mialsrtkGaussianDenoising 24 | mialsrtkTVDenoising 25 | DESTINATION 26 | bin) 27 | -------------------------------------------------------------------------------- /documentation/citing.rst: -------------------------------------------------------------------------------- 1 | .. _citing: 2 | 3 | ********* 4 | Citing 5 | ********* 6 | 7 | .. important:: 8 | * If your are using the MIALSRTK BIDS App, a manuscript is in preparation, but for now, please acknowledge this software with the following three entries: 9 | 10 | 1. Tourbier S, De Dumast P., Kebiri H., Sanchez T., Lajous H., Hagmann P., Bach Cuadra M. (2023, January 31). Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit: MIAL Super-Resolution Toolkit (Version v2.1.0). Zenodo. http://doi.org/10.5281/zenodo.4290209 11 | 12 | 2. Tourbier S, Bresson X, Hagmann P, Meuli R, Bach Cuadra M, *An efficient total variation algorithm for super-resolution in fetal brain MRI with adaptive regularization*, Neuroimage 118 (2015) 584-597. doi:10.1016/j.neuroimage.2015.06.018 13 | 14 | 3. Tourbier S, Velasco-Annis C, Taimouri V, Hagmann P, Meuli R, Warfield SK, Bach Cuadra M, A. Gholipour, *Automated template-based brain localization and extraction for fetal brain MRI reconstruction*, Neuroimage (2017) In Press. doi:10.1016/j.neuroimage.2017.04.004 15 | -------------------------------------------------------------------------------- /scripts/build_jupyter.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | SCRIPTSDIR=$(cd "$(dirname "$0")"; pwd) 3 | BASEDIR="$(dirname "$SCRIPTSDIR")" 4 | cd "$BASEDIR" 5 | 6 | CMP_BUILD_DATE="$(date -u +"%Y-%m-%dT%H:%M:%SZ")" 7 | echo "$CMP_BUILD_DATE" 8 | 9 | VERSION="v$(python get_version.py)" 10 | echo "$VERSION" 11 | 12 | VCS_REF="$(git rev-parse --verify HEAD)" 13 | echo "$VCS_REF" 14 | 15 | MAIN_DOCKER="sebastientourbier/mialsuperresolutiontoolkit-ubuntu14.04:${VERSION}" 16 | echo "$MAIN_DOCKER" 17 | 18 | docker build --rm --build-arg BUILD_DATE="$CMP_BUILD_DATE" \ 19 | --build-arg VCS_REF="$VCS_REF" \ 20 | --build-arg VERSION="$VERSION" \ 21 | -t "${MAIN_DOCKER}" "$BASEDIR" \ 22 | 23 | JUPYTER_DOCKER="sebastientourbier/mialsuperresolutiontoolkit-jupyter:${VERSION}" 24 | 25 | docker build --rm --build-arg BUILD_DATE="$CMP_BUILD_DATE" \ 26 | --build-arg VERSION="$VERSION" \ 27 | --build-arg VCS_REF="$VCS_REF" \ 28 | --build-arg MAIN_DOCKER="$MAIN_DOCKER" \ 29 | -t "${JUPYTER_DOCKER}" "$BASEDIR/docker/jupyter" 30 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/all_0.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
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25 | 26 | 27 | -------------------------------------------------------------------------------- /src/cmake_uninstall.cmake.in: -------------------------------------------------------------------------------- 1 | if(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt") 2 | message(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"") 3 | endif(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt") 4 | 5 | cmake_policy(SET CMP0007 OLD) 6 | 7 | file(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files) 8 | string(REGEX REPLACE "\n" ";" files "${files}") 9 | list(REVERSE files) 10 | foreach(file ${files}) 11 | message(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"") 12 | if(EXISTS "$ENV{DESTDIR}${file}") 13 | execute_process( 14 | COMMAND @CMAKE_COMMAND@ -E remove "$ENV{DESTDIR}${file}" 15 | OUTPUT_VARIABLE rm_out 16 | RESULT_VARIABLE rm_retval 17 | ) 18 | if(NOT ${rm_retval} EQUAL 0) 19 | message(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"") 20 | endif (NOT ${rm_retval} EQUAL 0) 21 | else(EXISTS "$ENV{DESTDIR}${file}") 22 | message(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.") 23 | endif(EXISTS "$ENV{DESTDIR}${file}") 24 | endforeach(file) 25 | 26 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/classes_0.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
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25 | 26 | 27 | -------------------------------------------------------------------------------- /src/BrainLocalizationExtraction/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(BrainLocalizationExtraction) 2 | INCLUDE_REGULAR_EXPRESSION("^.*$") 3 | 4 | INCLUDE_DIRECTORIES(${TCLAP_DIRECTORY}) 5 | INCLUDE_DIRECTORIES(${ANN_INCLUDE_DIR}) 6 | 7 | INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/CRKit) 8 | INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Maths) 9 | INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Transformations) 10 | 11 | ADD_EXECUTABLE(mialsrtkSegmentationWeightedFusion mialsrtkSegmentationWeightedFusion.cxx) 12 | TARGET_LINK_LIBRARIES(mialsrtkSegmentationWeightedFusion ${ITK_LIBRARIES}) 13 | 14 | ADD_EXECUTABLE(mialsrtkSegmentationWeightedFusionWithUnanimousConsensus mialsrtkSegmentationWeightedFusionWithUnanimousConsensus.cxx) 15 | TARGET_LINK_LIBRARIES(mialsrtkSegmentationWeightedFusionWithUnanimousConsensus ${ITK_LIBRARIES}) 16 | 17 | ADD_EXECUTABLE(mialsrtkRefineHRMaskByIntersection mialsrtkRefineHRMaskByIntersection.cxx) 18 | TARGET_LINK_LIBRARIES(mialsrtkRefineHRMaskByIntersection ${ITK_LIBRARIES}) 19 | 20 | 21 | 22 | INSTALL(TARGETS 23 | mialsrtkRefineHRMaskByIntersection 24 | mialsrtkSegmentationWeightedFusion 25 | mialsrtkSegmentationWeightedFusionWithUnanimousConsensus 26 | DESTINATION bin) 27 | 28 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/all_14.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['_7eboxcarpsf',['~BoxCarPSF',['../classbtk_1_1_box_car_p_s_f.html#adbee7dc0a88044e98cab5fd3748ad717',1,'btk::BoxCarPSF']]], 4 | ['_7ecropimageusingmaskfilter',['~CropImageUsingMaskFilter',['../classbtk_1_1_crop_image_using_mask_filter.html#ac53e3c7cda35da004a78aa3d5ae70718',1,'btk::CropImageUsingMaskFilter']]], 5 | 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-------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['patchdistance',['PatchDistance',['../classbtk_1_1_n_l_m_tool.html#a676e1d41924020e40343a9fbd9f14525',1,'btk::NLMTool']]], 4 | ['printinfo',['PrintInfo',['../classbtk_1_1_n_l_m_tool.html#a3b8f17cb21a93549286f26412ea849dd',1,'btk::NLMTool']]], 5 | ['printself',['PrintSelf',['../classbtk_1_1_box_car_p_s_f.html#a876bc4e75d06a54918a0c21db9f1f762',1,'btk::BoxCarPSF::PrintSelf()'],['../classbtk_1_1_gaussian_p_s_f.html#a121c9d54e22ba3d744745a1dc18768de',1,'btk::GaussianPSF::PrintSelf()'],['../classmialsrtk_1_1_b_spline_interpolate_image_function.html#a75f1ebdfb1ed38a1873aa885bbc9cff5',1,'mialsrtk::BSplineInterpolateImageFunction::PrintSelf()'],['../classmialsrtk_1_1_slice_by_slice_transform.html#af11d33baa5f169e3e327235cc68ced6c',1,'mialsrtk::SliceBySliceTransform::PrintSelf()'],['../classmialsrtk_1_1_slice_by_slice_transform_base.html#a07f76d52f6d461ad8aec363014f074e9',1,'mialsrtk::SliceBySliceTransformBase::PrintSelf()'],['../classmialsrtk_1_1_versor_slice_by_slice_transform.html#a6fce3c9a9f96201d43cf2c38714ea75e',1,'mialsrtk::VersorSliceBySliceTransform::PrintSelf()']]], 6 | ['psf',['PSF',['../classbtk_1_1_p_s_f.html#a5d76f6197589f8fc112c0f05af95aef1',1,'btk::PSF']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/functions_11.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['_7eboxcarpsf',['~BoxCarPSF',['../classbtk_1_1_box_car_p_s_f.html#adbee7dc0a88044e98cab5fd3748ad717',1,'btk::BoxCarPSF']]], 4 | ['_7ecropimageusingmaskfilter',['~CropImageUsingMaskFilter',['../classbtk_1_1_crop_image_using_mask_filter.html#ac53e3c7cda35da004a78aa3d5ae70718',1,'btk::CropImageUsingMaskFilter']]], 5 | ['_7egaussianpsf',['~GaussianPSF',['../classbtk_1_1_gaussian_p_s_f.html#a07a199da3b7183d6a6aadb17c6418847',1,'btk::GaussianPSF']]], 6 | ['_7eimageregistrationfilter',['~ImageRegistrationFilter',['../classmialsrtk_1_1_image_registration_filter.html#a9a83fa52d03c17906758db284bedc113',1,'mialsrtk::ImageRegistrationFilter']]], 7 | ['_7epsf',['~PSF',['../classbtk_1_1_p_s_f.html#a0efb043fbedc90e2f6162bcda3045d9f',1,'btk::PSF']]], 8 | ['_7eresampleimagestobiggestimagefilter',['~ResampleImagesToBiggestImageFilter',['../classbtk_1_1_resample_images_to_biggest_image_filter.html#ab93d11be81652b949d489a42dbeb83a9',1,'btk::ResampleImagesToBiggestImageFilter']]], 9 | ['_7eweightedsumofimagesfilter',['~WeightedSumOfImagesFilter',['../classbtk_1_1_weighted_sum_of_images_filter.html#a34eb432ba07ad27c607f4a5c8a80c881',1,'btk::WeightedSumOfImagesFilter']]] 10 | ]; 11 | -------------------------------------------------------------------------------- /pymialsrtk/sphinxext/gh.py: -------------------------------------------------------------------------------- 1 | """Build a file URL.""" 2 | import os 3 | import inspect 4 | import subprocess 5 | 6 | REVISION_CMD = "git rev-parse --short HEAD" 7 | 8 | 9 | def _get_git_revision(): 10 | # Comes from scikit-learn 11 | # https://github.com/scikit-learn/scikit-learn/blob/master/doc/sphinxext/github_link.py 12 | try: 13 | revision = subprocess.check_output(REVISION_CMD.split()).strip() 14 | except (subprocess.CalledProcessError, OSError): 15 | return None 16 | return revision.decode("utf-8") 17 | 18 | 19 | def get_url(obj): 20 | """Return local or remote url for an object.""" 21 | # Comes from Nipype 22 | # https://github.com/nipy/nipype/blob/master/nipype/sphinxext/gh.py 23 | # URL was updated to http://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit 24 | filename = inspect.getsourcefile(obj) 25 | uri = "file://%s" % filename 26 | revision = _get_git_revision() 27 | if revision is not None: 28 | shortfile = os.path.join("pymialsrtk", filename.split("pymialsrtk/")[-1]) 29 | uri = "http://github.com/Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit/blob/%s/%s" % (revision, shortfile) 30 | lines, lstart = inspect.getsourcelines(obj) 31 | lend = len(lines) + lstart 32 | return "%s#L%d-L%d" % (uri, lstart, lend) 33 | -------------------------------------------------------------------------------- /docker/jupyter/environment.yml: -------------------------------------------------------------------------------- 1 | name: pymialsrtk-env 2 | 3 | channels: 4 | - anaconda 5 | - conda-forge 6 | - defaults 7 | 8 | dependencies: 9 | - python=3.6.8 10 | - pip=19.0.3 11 | #- git-annex=7.20190219 12 | - nibabel=3.0.1 13 | - nipype=1.5.1 14 | - traits=5.1.2 15 | - traitsui=6.0.0 16 | - jupyter=1.0.0 17 | - jupyterlab=1.1.3 18 | #- matplotlib=2.2.3 19 | #- graphviz=2.40.1 20 | - pyface=7.0.0 21 | - pydotplus=2.0.2 22 | - pandoc=2.11.0.1 23 | 24 | - pip: 25 | - coverage==5.1 26 | - duecredit==0.8.0 27 | - apptools==4.4.0 28 | # - niworkflows==0.10.2 29 | - graphviz 30 | - numpy==1.16.4 # numpy 1.18.5 caused error (fix: https://github.com/DeepLabCut/Docker4DeepLabCut2.0/issues/26) 31 | - tensorflow==1.13.1 # https://storage.googleapis.com/tensorflow/linux/cpu/tensorflow-1.1.0-cp36-cp36m-linux_x86_64.whl # tensorflow==1.15 # tflearn needs tensorflow 1.0+ 32 | - tensorflow-estimator==1.13.0 33 | - tensorboard==1.13.1 34 | - tflearn==0.3.2 35 | - MedPy==0.4.0 36 | - opencv-python==4.1.0.25 37 | - scikit-learn==0.20.3 38 | - scikit-image==0.14.2 39 | - sphinx==1.8.5 40 | - sphinx_rtd_theme==0.4.3 41 | - sphinx-argparse==0.2.5 42 | - nbsphinx==0.7.1 43 | - recommonmark==0.5.0 44 | - jupyter_contrib_nbextensions #==0.5.1 45 | # - pybids==0.9.1 46 | - matplotlib==3.4 47 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | dist: trusty 2 | sudo: required 3 | language: 4 | - cpp 5 | compiler: 6 | - gcc 7 | addons: 8 | apt: 9 | sources: 10 | - ubuntu-toolchain-r-test 11 | packages: 12 | - gcc-4.8 13 | - g++-4.8 14 | - cmake 15 | - libtclap-dev 16 | - libinsighttoolkit4.5 17 | - libinsighttoolkit4-dev 18 | - libvtk5-dev 19 | - libvtk5-qt4-dev 20 | - libvtk5.8 21 | - libvtk5.8-qt4 22 | - tcl-vtk 23 | - libvtk-java 24 | - python-vtk 25 | - python-vtkgdcm 26 | - libncurses5 27 | - libncurses5-dev 28 | - libann-dev 29 | #- libgdcm2-dev 30 | #- libvtkgdcm2-dev 31 | #- libgdcm-tools 32 | #- libvtkgdcm-tools 33 | 34 | #before_script: 35 | # - mkdir build 36 | # - cd build 37 | # - cmake ../src 38 | script: 39 | # Link gcc-4.8 and g++-4.8 to their standard commands 40 | - sudo ln -s /usr/bin/gcc-4.8 /usr/local/bin/gcc 41 | - sudo ln -s /usr/bin/g++-4.8 /usr/local/bin/g++ 42 | # Export CC and CXX to tell cmake which compiler to use 43 | - export CC=/usr/bin/gcc-4.8 44 | - export CXX=/usr/bin/g++-4.8 45 | # Check versions of gcc, g++ and cmake 46 | - gcc -v && g++ -v && cmake --version 47 | # Run your build commands next 48 | - mkdir build 49 | - cd build 50 | - cmake ../src -DUSE_OMP:BOOL=ON 51 | - make 52 | -------------------------------------------------------------------------------- /src/SuperResolution/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(Applications) 2 | INCLUDE_REGULAR_EXPRESSION("^.*$") 3 | 4 | #message(STATUS BTK_SRC_DIR=${BTK_SRC_DIR}) 5 | 6 | INCLUDE_DIRECTORIES( 7 | ${TCLAP_DIRECTORY} 8 | ) 9 | 10 | #---- Set BTK library DIR --------------------------------------------------------------------- 11 | #LINK_DIRECTORIES(${BTK_BIN_DIR}/Code) 12 | 13 | # ---- Reconstruction ------------------------------------------------------------------- 14 | # BTK 15 | INCLUDE_DIRECTORIES( 16 | ${ANN_INCLUDE_DIR} 17 | ${CMAKE_SOURCE_DIR}/Code/BTK 18 | ) 19 | 20 | #MIALTK 21 | INCLUDE_DIRECTORIES( 22 | ${CMAKE_SOURCE_DIR}/Code/Maths 23 | ${CMAKE_SOURCE_DIR}/Code/Evaluation 24 | ${CMAKE_SOURCE_DIR}/Code/Reconstruction 25 | ${CMAKE_SOURCE_DIR}/Code/Registration 26 | ${CMAKE_SOURCE_DIR}/Code/Transformations 27 | ${CMAKE_SOURCE_DIR}/Code/Timer 28 | ) 29 | 30 | 31 | ADD_EXECUTABLE(mialsrtkTVSuperResolution mialsrtkTVSuperResolution.cxx) 32 | TARGET_LINK_LIBRARIES(mialsrtkTVSuperResolution ${ITK_LIBRARIES}) 33 | 34 | ADD_EXECUTABLE(mialsrtkRobustTVSuperResolutionWithGMM mialsrtkRobustTVSuperResolutionWithGMM.cxx) 35 | TARGET_LINK_LIBRARIES(mialsrtkRobustTVSuperResolutionWithGMM ${ITK_LIBRARIES}) 36 | 37 | 38 | INSTALL(TARGETS 39 | mialsrtkTVSuperResolution 40 | mialsrtkRobustTVSuperResolutionWithGMM 41 | DESTINATION bin) 42 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/all_12.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['vectorimageiteratortype',['VectorImageIteratorType',['../classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.html#acfc6c58be7b7cb7df3bf0b92ab164b9e',1,'mialsrtk::RobustSuperResolutionRigidImageFilterWithGMM']]], 4 | ['verifyinputinformation',['VerifyInputInformation',['../classmialsrtk_1_1_resample_image_by_injection_filter.html#a90f9049d6064a0fa4d6e362f6fd56fa8',1,'mialsrtk::ResampleImageByInjectionFilter']]], 5 | 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/documentation/doxygen_html/tabs.css: -------------------------------------------------------------------------------- 1 | .tabs, .tabs2, .tabs3 { 2 | background-image: url('tab_b.png'); 3 | width: 100%; 4 | z-index: 101; 5 | font-size: 13px; 6 | font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif; 7 | } 8 | 9 | .tabs2 { 10 | font-size: 10px; 11 | } 12 | .tabs3 { 13 | font-size: 9px; 14 | } 15 | 16 | .tablist { 17 | margin: 0; 18 | padding: 0; 19 | display: table; 20 | } 21 | 22 | .tablist li { 23 | float: left; 24 | display: table-cell; 25 | background-image: url('tab_b.png'); 26 | line-height: 36px; 27 | list-style: none; 28 | } 29 | 30 | .tablist a { 31 | display: block; 32 | padding: 0 20px; 33 | font-weight: bold; 34 | background-image:url('tab_s.png'); 35 | background-repeat:no-repeat; 36 | background-position:right; 37 | color: #283A5D; 38 | text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9); 39 | text-decoration: none; 40 | outline: none; 41 | } 42 | 43 | .tabs3 .tablist a { 44 | padding: 0 10px; 45 | } 46 | 47 | .tablist a:hover { 48 | background-image: url('tab_h.png'); 49 | background-repeat:repeat-x; 50 | color: #fff; 51 | text-shadow: 0px 1px 1px rgba(0, 0, 0, 1.0); 52 | text-decoration: none; 53 | } 54 | 55 | .tablist li.current a { 56 | background-image: url('tab_a.png'); 57 | background-repeat:repeat-x; 58 | color: #fff; 59 | text-shadow: 0px 1px 1px rgba(0, 0, 0, 1.0); 60 | } 61 | -------------------------------------------------------------------------------- /pymialsrtk/info.py: -------------------------------------------------------------------------------- 1 | """This file contains MIALSRTK package information.""" 2 | 3 | _version_major = 2 4 | _version_minor = 1 5 | _version_micro = 0 6 | _version_extra = '' 7 | 8 | __release_date__ = '11.01.2023' 9 | 10 | __minor_version__ = "%s.%s" % (_version_major, 11 | _version_minor) 12 | 13 | __version__ = "%s.%s.%s%s" % (_version_major, 14 | _version_minor, 15 | _version_micro, 16 | _version_extra) 17 | 18 | # __current_year__ = datetime.datetime.now().strftime("%Y") 19 | __current_year__ = '2023' 20 | 21 | __author__ = 'The MIAL Super-Resolution ToolKit developers' 22 | __copyright__ = 'Copyright 2016-{}, Medical Image Analysis Laboratory (MIAL), Lausanne'.format(__current_year__) 23 | __credits__ = ('Contributors: please check the ``.zenodo.json`` file at the top-level folder' 24 | 'of the repository') 25 | __license__ = '3-clause BSD' 26 | __maintainer__ = 'Sebastien Tourbier' 27 | __email__ = 'sebastien.tourbier@alumni.epfl.ch' 28 | __status__ = 'Prototype' 29 | 30 | __packagename__ = 'mialsuperresolutiontoolkit' 31 | 32 | __url__ = 'https://github.com/sebastientourbier/{name}'.format(name=__packagename__) 33 | 34 | DOWNLOAD_URL = ( 35 | 'https://github.com/sebastientourbier/{name}/archive/{ver}.tar.gz'.format( 36 | name=__packagename__, ver=__version__)) 37 | 38 | DOCKER_HUB = 'sebastientourbier/mialsuperresolutiontoolkit' 39 | 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################### 3 | *.com 4 | *.class 5 | *.dll 6 | *.exe 7 | *.o 8 | *.so 9 | *.*~ 10 | *.save 11 | 12 | # python # 13 | ################################# 14 | *.ipynb_checkpoints 15 | *__pycache__ 16 | 17 | # Generated testing images # 18 | ############################ 19 | superresolution.nii.gz 20 | superresolution_masked.nii.gz 21 | 22 | # LATEX # 23 | ######### 24 | *.tex.backup 25 | *.aux 26 | *.toc 27 | *.kilepr 28 | *.bbl 29 | *.dvi 30 | *.ps 31 | *.blg 32 | *.out 33 | 34 | # Packages # 35 | ############ 36 | # it's better to unpack these files and commit the raw source 37 | # git has its own built in compression methods 38 | *.7z 39 | *.dmg 40 | #*.gz 41 | *.iso 42 | *.jar 43 | *.rar 44 | *.tar 45 | *.zip 46 | 47 | # Logs and databases # 48 | ###################### 49 | *.log 50 | *.sql 51 | *.sqlite 52 | 53 | # OS generated files # 54 | ###################### 55 | .DS_Store? 56 | .DS_Store 57 | ehthumbs.db 58 | Icon? 59 | Thumbs.db 60 | 61 | # QtCreator generated files # 62 | ############################# 63 | CMakeLists.txt.user* 64 | 65 | # Build directories # 66 | ##################### 67 | debug 68 | Build 69 | Build-dbg 70 | Build-debug 71 | build 72 | build-dbg 73 | build-debug 74 | _build 75 | release 76 | bin 77 | bin-dbg 78 | Bin 79 | RECON 80 | dist 81 | *egg-info/* 82 | 83 | # Data derivatives # 84 | ##################### 85 | data/derivatives/mialsrtk* 86 | data/derivatives/nipype* 87 | data/derivatives/pymialsrtk* 88 | data/derivatives/manual_masks* 89 | data/sub-ctrl* 90 | 91 | # Editors # 92 | ##################### 93 | .idea/* 94 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/all_5.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | 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If True, only the diff is scanned. 5 | linter: pycodestyle # Other option is flake8 6 | 7 | pycodestyle: # Same as scanner.linter value. Other option is pycodestyle 8 | max-line-length: 119 # Default is 79 in PEP 8 9 | ignore: # Errors and warnings to ignore 10 | - W504 # line break after binary operator 11 | - E402 # module level import not at top of file 12 | - E731 # do not assign a lambda expression, use a def 13 | - C406 # Unnecessary list literal - rewrite as a dict literal. 14 | - E741 # ambiguous variable name 15 | 16 | no_blank_comment: True # If True, no comment is made on PR without any errors. 17 | descending_issues_order: False # If True, PEP 8 issues in message will be displayed in descending order of line numbers in the file 18 | 19 | message: # Customize the comment made by the bot 20 | opened: # Messages when a new PR is submitted 21 | header: "Hello @{name}! Thanks for opening this PR. " 22 | # The keyword {name} is converted into the author's username 23 | footer: "Do see the [Hitchhiker's guide to code style](https://goo.gl/hqbW4r)" 24 | # The messages can be written as they would over GitHub 25 | updated: # Messages when new commits are added to the PR 26 | header: "Hello @{name}! Thanks for updating this PR. " 27 | footer: "" # Why to comment the link to the style guide everytime? :) 28 | no_errors: "There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers: " 29 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2012-2017, Medical Image Analysis Laboratory (MIAL) - University and University Hospital Center of Lausanne (UNIL-CHUV), Switzerland 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | * Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 12 | * Redistributions in binary form must reproduce the above copyright notice, 13 | this list of conditions and the following disclaimer in the documentation 14 | and/or other materials provided with the distribution. 15 | 16 | * Neither the name of the copyright holder nor the names of its 17 | contributors may be used to endorse or promote products derived from 18 | this software without specific prior written permission. 19 | 20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 30 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/all_13.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['weightedsumofimagesfilter',['WeightedSumOfImagesFilter',['../classbtk_1_1_weighted_sum_of_images_filter.html',1,'btk']]], 4 | ['weightedsumofimagesfilter',['WeightedSumOfImagesFilter',['../classbtk_1_1_weighted_sum_of_images_filter.html#adfbc9879a9464f43b5d127e3d62a7f51',1,'btk::WeightedSumOfImagesFilter']]], 5 | ['writeimage',['WriteImage',['../classbtk_1_1_image_helper.html#afbd660d49b50e643d0042bf18165e2dd',1,'btk::ImageHelper::WriteImage(typename TImageInput::Pointer image, const std::string &fileName)'],['../classbtk_1_1_image_helper.html#af7cc85cb8cf89a334a10e3b4d8b380af',1,'btk::ImageHelper::WriteImage(std::vector< typename TImageInput::Pointer > &images, std::vector< std::string > &fileNames)']]], 6 | ['writemask',['WriteMask',['../classmialsrtk_1_1_image_intersection_calculator.html#a954c6dadae140f16f50548659c8037eb',1,'mialsrtk::ImageIntersectionCalculator']]], 7 | ['writeresampledimages',['WriteResampledImages',['../classmialsrtk_1_1_low_to_high_image_resolution_method.html#a49d3cae848b2679f30e4f3304d976d05',1,'mialsrtk::LowToHighImageResolutionMethod::WriteResampledImages(const char *folder)'],['../classmialsrtk_1_1_low_to_high_image_resolution_method.html#a6e4b213ffbc5a59966269b90934732bf',1,'mialsrtk::LowToHighImageResolutionMethod::WriteResampledImages(unsigned int i, const char *filename)']]], 8 | ['writetransforms',['WriteTransforms',['../classmialsrtk_1_1_low_to_high_image_resolution_method.html#a8fa112144ffd7b1139c6e4f9bc54a92b',1,'mialsrtk::LowToHighImageResolutionMethod::WriteTransforms(const char *folder)'],['../classmialsrtk_1_1_low_to_high_image_resolution_method.html#ac60ccfb19e9c7736688ea486635037a5',1,'mialsrtk::LowToHighImageResolutionMethod::WriteTransforms(unsigned int i, const char *filename)']]] 9 | ]; 10 | -------------------------------------------------------------------------------- /documentation/LICENSE.rst: -------------------------------------------------------------------------------- 1 | .. _LICENSE: 2 | 3 | BSD 3-Clause License 4 | ======================================================= 5 | 6 | Copyright (c) 2012-2020, Medical Image Analysis Laboratory (MIAL) - University and University Hospital Center of Lausanne (UNIL-CHUV), Switzerland 7 | All rights reserved. 8 | 9 | Redistribution and use in source and binary forms, with or without 10 | modification, are permitted provided that the following conditions are met: 11 | 12 | * Redistributions of source code must retain the above copyright notice, this 13 | list of conditions and the following disclaimer. 14 | 15 | * Redistributions in binary form must reproduce the above copyright notice, 16 | this list of conditions and the following disclaimer in the documentation 17 | and/or other materials provided with the distribution. 18 | 19 | * Neither the name of the copyright holder nor the names of its 20 | contributors may be used to endorse or promote products derived from 21 | this software without specific prior written permission. 22 | 23 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 24 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 25 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 26 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 27 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 28 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 29 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 30 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 31 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 32 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 33 | 34 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/typedefs_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['coefficientdatatype',['CoefficientDataType',['../classmialsrtk_1_1_b_spline_interpolate_image_function.html#a5e110f028266ae9747e463f69c10e48a',1,'mialsrtk::BSplineInterpolateImageFunction']]], 4 | 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['pointtype',['PointType',['../classbtk_1_1_p_s_f.html#aa1599beb13d31bea49759d461edb87d0',1,'btk::PSF::PointType()'],['../classmialsrtk_1_1_oriented_spatial_function.html#a87c8aeb6c2dd60d8bd1e224a1d722d75',1,'mialsrtk::OrientedSpatialFunction::PointType()'],['../classmialsrtk_1_1_resample_image_by_injection_filter.html#a271de02a2e8fb805baa89161581ffa7e',1,'mialsrtk::ResampleImageByInjectionFilter::PointType()'],['../classmialsrtk_1_1_robust_super_resolution_rigid_image_filter_with_g_m_m.html#a75d7ef39d38973f72b5e0c07d5f6230a',1,'mialsrtk::RobustSuperResolutionRigidImageFilterWithGMM::PointType()'],['../classmialsrtk_1_1_super_resolution_rigid_image_filter_with_implicit_gradient_descent.html#aaa73761fbbff0c8ed866f89cddc99280',1,'mialsrtk::SuperResolutionRigidImageFilterWithImplicitGradientDescent::PointType()'],['../classmialsrtk_1_1_b_spline_interpolate_image_function.html#a7098de7e54afa6a342ef7a8e7679e47f',1,'mialsrtk::BSplineInterpolateImageFunction::PointType()'],['../classmialsrtk_1_1_rigid_registration.html#ac2b5e0a2de2fe37756bb15880c604f16',1,'mialsrtk::RigidRegistration::PointType()']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /src/Tools/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(Utilities) 2 | INCLUDE_REGULAR_EXPRESSION("^.*$") 3 | 4 | INCLUDE_DIRECTORIES(${TCLAP_DIRECTORY}) 5 | INCLUDE_DIRECTORIES(${ANN_INCLUDE_DIR}) 6 | INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/BTK) 7 | INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Maths) 8 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Reconstruction) 9 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Transformations) 10 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Maths) 11 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Registration) 12 | # INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Maths) 13 | 14 | ADD_EXECUTABLE(mialsrtkComputeVolume mialsrtkComputeVolume.cxx) 15 | TARGET_LINK_LIBRARIES(mialsrtkComputeVolume ${ITK_LIBRARIES}) 16 | 17 | ADD_EXECUTABLE(mialsrtkCropImageUsingMask mialsrtkCropImageUsingMask.cxx) 18 | TARGET_LINK_LIBRARIES(mialsrtkCropImageUsingMask ${ITK_LIBRARIES}) 19 | 20 | ADD_EXECUTABLE(mialsrtkCreateImageWithHalo mialsrtkCreateImageWithHalo.cxx) 21 | TARGET_LINK_LIBRARIES(mialsrtkCreateImageWithHalo ${ITK_LIBRARIES}) 22 | 23 | ADD_EXECUTABLE(mialsrtkCreateWhiteMatterVolumeFromLabels mialsrtkCreateWhiteMatterVolumeFromLabels.cxx) 24 | TARGET_LINK_LIBRARIES(mialsrtkCreateWhiteMatterVolumeFromLabels ${ITK_LIBRARIES}) 25 | 26 | ADD_EXECUTABLE(mialsrtkFourierTransform mialsrtkFourierTransform.cxx) 27 | TARGET_LINK_LIBRARIES(mialsrtkFourierTransform ${ITK_LIBRARIES}) 28 | 29 | ADD_EXECUTABLE(mialsrtkMaskImage mialsrtkMaskImage.cxx) 30 | TARGET_LINK_LIBRARIES(mialsrtkMaskImage ${ITK_LIBRARIES}) 31 | 32 | ADD_EXECUTABLE(mialsrtkOrientImage mialsrtkOrientImage.cxx) 33 | TARGET_LINK_LIBRARIES(mialsrtkOrientImage ${ITK_LIBRARIES}) 34 | 35 | 36 | INSTALL(TARGETS 37 | mialsrtkCreateImageWithHalo 38 | mialsrtkCreateWhiteMatterVolumeFromLabels 39 | mialsrtkCropImageUsingMask 40 | mialsrtkCropImageUsingMask 41 | mialsrtkFourierTransform 42 | mialsrtkMaskImage 43 | mialsrtkOrientImage 44 | DESTINATION bin) 45 | 46 | -------------------------------------------------------------------------------- /documentation/doxygen_html/search/typedefs_c.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['transforminitializertype',['TransformInitializerType',['../classmialsrtk_1_1_rigid_registration.html#a847ea736c4826bafe7ca6a574f908c2f',1,'mialsrtk::RigidRegistration']]], 4 | 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7 | ]; 8 | -------------------------------------------------------------------------------- /src/Evaluation/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | PROJECT(Evaluation) 2 | INCLUDE_REGULAR_EXPRESSION("^.*$") 3 | 4 | INCLUDE_DIRECTORIES(${TCLAP_DIRECTORY}) 5 | INCLUDE_DIRECTORIES(${ANN_INCLUDE_DIR}) 6 | 7 | INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Code/Maths) 8 | 9 | ADD_EXECUTABLE(mialsrtkComputeHistogramSpread mialsrtkComputeHistogramSpread.cxx) 10 | IF(CMAKE_SYSTEM_NAME STREQUAL Linux) 11 | TARGET_LINK_LIBRARIES(mialsrtkComputeHistogramSpread ${ITK_LIBRARIES} rt) 12 | ENDIF(CMAKE_SYSTEM_NAME STREQUAL Linux) 13 | IF(CMAKE_SYSTEM_NAME STREQUAL Darwin) 14 | TARGET_LINK_LIBRARIES(mialsrtkComputeHistogramSpread ${ITK_LIBRARIES}) 15 | ENDIF(CMAKE_SYSTEM_NAME STREQUAL Darwin) 16 | 17 | 18 | ADD_EXECUTABLE(mialsrtkEvaluateContrast mialsrtkEvaluateContrast.cxx) 19 | TARGET_LINK_LIBRARIES(mialsrtkEvaluateContrast ${ITK_LIBRARIES}) 20 | 21 | ADD_EXECUTABLE(mialsrtkComputeImageMedianCNR mialsrtkComputeImageMedianCNR.cxx) 22 | TARGET_LINK_LIBRARIES(mialsrtkComputeImageMedianCNR ${ITK_LIBRARIES}) 23 | 24 | ADD_EXECUTABLE(mialsrtkComputeHausdorffDistance mialsrtkComputeHausdorffDistance.cxx) 25 | TARGET_LINK_LIBRARIES(mialsrtkComputeHausdorffDistance ${ITK_LIBRARIES}) 26 | 27 | ADD_EXECUTABLE(mialsrtkEvaluateLabelOverlapMeasures mialsrtkEvaluateLabelOverlapMeasures.cxx) 28 | TARGET_LINK_LIBRARIES(mialsrtkEvaluateLabelOverlapMeasures ${ITK_LIBRARIES}) 29 | 30 | ADD_EXECUTABLE(mialsrtkEvaluateSharpnessMeasures mialsrtkEvaluateSharpnessMeasures.cxx) 31 | TARGET_LINK_LIBRARIES(mialsrtkEvaluateSharpnessMeasures ${ITK_LIBRARIES}) 32 | 33 | ADD_EXECUTABLE(mialsrtkEvaluateReconstructionQualityMeasures mialsrtkEvaluateReconstructionQualityMeasures.cxx) 34 | TARGET_LINK_LIBRARIES(mialsrtkEvaluateReconstructionQualityMeasures ${ITK_LIBRARIES} ${VTK_LIBRARIES}) 35 | 36 | INSTALL(TARGETS 37 | mialsrtkComputeHausdorffDistance 38 | mialsrtkComputeHistogramSpread 39 | mialsrtkComputeImageMedianCNR 40 | mialsrtkEvaluateContrast 41 | mialsrtkEvaluateLabelOverlapMeasures 42 | mialsrtkEvaluateSharpnessMeasures 43 | mialsrtkEvaluateReconstructionQualityMeasures 44 | 45 | DESTINATION bin) 46 | 47 | -------------------------------------------------------------------------------- /data/sub-01/anat/sub-01_run-1_T2w.json: -------------------------------------------------------------------------------- 1 | { 2 | "Modality": "MR", 3 | "MagneticFieldStrength": 1.5, 4 | "ImagingFrequency": 63.6693, 5 | "Manufacturer": "Siemens", 6 | "ManufacturersModelName": "Aera", 7 | "InstitutionName": "Radiologie_CHUV", 8 | "InstitutionalDepartmentName": "Radiodiagnostic", 9 | "InstitutionAddress": "Rue_du_Bugnon_21_Lausanne_District_CH_1011", 10 | "DeviceSerialNumber": "41200", 11 | "StationName": "AWP41200", 12 | "BodyPartExamined": "ABDOMENPELVIS", 13 | "PatientPosition": "HFS", 14 | "ProcedureStepDescription": "IRM_FOETALE", 15 | "SoftwareVersions": "syngo_MR_E11", 16 | "MRAcquisitionType": "2D", 17 | "SeriesDescription": "T2_haste_3mm", 18 | "ProtocolName": "T2_haste_3mm", 19 | "ScanningSequence": "SE", 20 | "SequenceVariant": "SK_SP_OSP", 21 | "ScanOptions": "PFP", 22 | "SequenceName": "_h2d1_224", 23 | "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"], 24 | "SeriesNumber": 2, 25 | "AcquisitionTime": "17:00:58.777500", 26 | "AcquisitionNumber": 1, 27 | "SliceThickness": 3, 28 | "SpacingBetweenSlices": 3.3, 29 | "SAR": 2, 30 | "EchoTime": 0.09, 31 | "RepetitionTime": 1.2, 32 | "FlipAngle": 167, 33 | "PartialFourier": 0.5, 34 | "BaseResolution": 320, 35 | "ShimSetting": [ 36 | -888, 37 | 5, 38 | 4578, 39 | -1465, 40 | -48, 41 | 13, 42 | 19, 43 | 132 ], 44 | "TxRefAmp": 362.247, 45 | "PhaseResolution": 0.7, 46 | "PhaseOversampling": 0.8, 47 | "ReceiveCoilName": "Spine_32", 48 | "ReceiveCoilActiveElements": "BO1-3;SP3-5", 49 | "PulseSequenceDetails": "%SiemensSeq%_haste", 50 | "ConsistencyInfo": "N4_VE11A_LATEST_20140830", 51 | "PercentPhaseFOV": 100, 52 | "EchoTrainLength": 134, 53 | "PhaseEncodingSteps": 225, 54 | "AcquisitionMatrixPE": 224, 55 | "ReconMatrixPE": 320, 56 | "ParallelReductionFactorInPlane": 2, 57 | "PixelBandwidth": 710, 58 | "DwellTime": 2.2e-06, 59 | "PhaseEncodingDirection": "i", 60 | "SliceTiming": [ 61 | ], 62 | "ImageOrientationPatientDICOM": [ 63 | 0.118404, 64 | 0.992966, 65 | -4.35961e-10, 66 | 0.0294575, 67 | -0.0035126, 68 | -0.99956 ], 69 | "InPlanePhaseEncodingDirectionDICOM": "ROW", 70 | "ConversionSoftware": "dcm2niix", 71 | "ConversionSoftwareVersion": "v1.0.20181125 GCC5.3.1" 72 | } 73 | -------------------------------------------------------------------------------- /data/sub-01/anat/sub-01_run-2_T2w.json: -------------------------------------------------------------------------------- 1 | { 2 | "Modality": "MR", 3 | "MagneticFieldStrength": 1.5, 4 | "ImagingFrequency": 63.6693, 5 | "Manufacturer": "Siemens", 6 | "ManufacturersModelName": "Aera", 7 | "InstitutionName": "Radiologie_CHUV", 8 | "InstitutionalDepartmentName": "Radiodiagnostic", 9 | "InstitutionAddress": "Rue_du_Bugnon_21_Lausanne_District_CH_1011", 10 | "DeviceSerialNumber": "41200", 11 | "StationName": "AWP41200", 12 | "BodyPartExamined": "ABDOMENPELVIS", 13 | "PatientPosition": "HFS", 14 | "ProcedureStepDescription": "IRM_FOETALE", 15 | "SoftwareVersions": "syngo_MR_E11", 16 | "MRAcquisitionType": "2D", 17 | "SeriesDescription": "T2_haste_3mm", 18 | "ProtocolName": "T2_haste_3mm", 19 | "ScanningSequence": "SE", 20 | "SequenceVariant": "SK_SP_OSP", 21 | "ScanOptions": "PFP", 22 | "SequenceName": "_h2d1_224", 23 | "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"], 24 | "SeriesNumber": 3, 25 | "AcquisitionTime": "17:01:58.207500", 26 | "AcquisitionNumber": 1, 27 | "SliceThickness": 3, 28 | "SpacingBetweenSlices": 3.3, 29 | "SAR": 2, 30 | "EchoTime": 0.09, 31 | "RepetitionTime": 1.2, 32 | "FlipAngle": 167, 33 | "PartialFourier": 0.5, 34 | "BaseResolution": 320, 35 | "ShimSetting": [ 36 | -888, 37 | 5, 38 | 4578, 39 | -1465, 40 | -48, 41 | 13, 42 | 19, 43 | 132 ], 44 | "TxRefAmp": 362.247, 45 | "PhaseResolution": 0.7, 46 | "PhaseOversampling": 0.8, 47 | "ReceiveCoilName": "Spine_32", 48 | "ReceiveCoilActiveElements": "BO1-3;SP3-5", 49 | "PulseSequenceDetails": "%SiemensSeq%_haste", 50 | "ConsistencyInfo": "N4_VE11A_LATEST_20140830", 51 | "PercentPhaseFOV": 100, 52 | "EchoTrainLength": 134, 53 | "PhaseEncodingSteps": 225, 54 | "AcquisitionMatrixPE": 224, 55 | "ReconMatrixPE": 320, 56 | "ParallelReductionFactorInPlane": 2, 57 | "PixelBandwidth": 710, 58 | "DwellTime": 2.2e-06, 59 | "PhaseEncodingDirection": "i", 60 | "SliceTiming": [ 61 | ], 62 | "ImageOrientationPatientDICOM": [ 63 | 0.118404, 64 | 0.992966, 65 | -4.35961e-10, 66 | 0.0294575, 67 | -0.0035126, 68 | -0.99956 ], 69 | "InPlanePhaseEncodingDirectionDICOM": "ROW", 70 | "ConversionSoftware": "dcm2niix", 71 | "ConversionSoftwareVersion": "v1.0.20181125 GCC5.3.1" 72 | } 73 | -------------------------------------------------------------------------------- /data/sub-01/anat/sub-01_run-5_T2w.json: -------------------------------------------------------------------------------- 1 | { 2 | "Modality": "MR", 3 | "MagneticFieldStrength": 1.5, 4 | "ImagingFrequency": 63.6693, 5 | "Manufacturer": "Siemens", 6 | "ManufacturersModelName": "Aera", 7 | "InstitutionName": "Radiologie_CHUV", 8 | "InstitutionalDepartmentName": "Radiodiagnostic", 9 | "InstitutionAddress": "Rue_du_Bugnon_21_Lausanne_District_CH_1011", 10 | "DeviceSerialNumber": "41200", 11 | "StationName": "AWP41200", 12 | "BodyPartExamined": "ABDOMENPELVIS", 13 | "PatientPosition": "HFS", 14 | "ProcedureStepDescription": "IRM_FOETALE", 15 | "SoftwareVersions": "syngo_MR_E11", 16 | "MRAcquisitionType": "2D", 17 | "SeriesDescription": "T2_haste_3mm", 18 | "ProtocolName": "T2_haste_3mm", 19 | "ScanningSequence": "SE", 20 | "SequenceVariant": "SK_SP_OSP", 21 | "ScanOptions": "PFP", 22 | "SequenceName": "_h2d1_224", 23 | "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"], 24 | "SeriesNumber": 6, 25 | "AcquisitionTime": "17:05:12.380000", 26 | "AcquisitionNumber": 1, 27 | "SliceThickness": 3, 28 | "SpacingBetweenSlices": 3.3, 29 | "SAR": 2, 30 | "EchoTime": 0.09, 31 | "RepetitionTime": 1.2, 32 | "FlipAngle": 168, 33 | "PartialFourier": 0.5, 34 | "BaseResolution": 320, 35 | "ShimSetting": [ 36 | -888, 37 | 5, 38 | 4578, 39 | -1465, 40 | -48, 41 | 13, 42 | 19, 43 | 132 ], 44 | "TxRefAmp": 360.391, 45 | "PhaseResolution": 0.7, 46 | "PhaseOversampling": 0.8, 47 | "ReceiveCoilName": "Spine_32", 48 | "ReceiveCoilActiveElements": "BO1-3;SP3-5", 49 | "PulseSequenceDetails": "%SiemensSeq%_haste", 50 | "ConsistencyInfo": "N4_VE11A_LATEST_20140830", 51 | "PercentPhaseFOV": 100, 52 | "EchoTrainLength": 134, 53 | "PhaseEncodingSteps": 225, 54 | "AcquisitionMatrixPE": 224, 55 | "ReconMatrixPE": 320, 56 | "ParallelReductionFactorInPlane": 2, 57 | "PixelBandwidth": 710, 58 | "DwellTime": 2.2e-06, 59 | "PhaseEncodingDirection": "i", 60 | "SliceTiming": [ 61 | ], 62 | "ImageOrientationPatientDICOM": [ 63 | 0.992879, 64 | -0.119124, 65 | 2.97176e-09, 66 | -0.00290917, 67 | -0.0242476, 68 | -0.999702 ], 69 | "InPlanePhaseEncodingDirectionDICOM": "ROW", 70 | "ConversionSoftware": "dcm2niix", 71 | "ConversionSoftwareVersion": "v1.0.20181125 GCC5.3.1" 72 | } 73 | --------------------------------------------------------------------------------