shimming-toolbox Logo

Overview

  • Welcome to shimming-toolbox!
    • Features
    • Installation
    • Usage

User Section

  • Installation
    • Installation on macOS and Linux
      • Dependencies
      • Installation Procedure for macOS and Linux
      • Test the Installation
        • Comprehensive Test
        • Testing subsets of soft dependencies
      • For Developers
        • Quick setup
        • Permanent setup
    • Installation on Windows
      • Dependencies
      • Installation Procedure for Windows
      • Test the Installation
        • Comprehensive Test
        • Testing subsets of soft dependencies
      • For Developers
  • Tutorials
    • Dynamic Shimming Tutorial
      • Download test data
      • Launch the plugin
      • Create a Fieldmap
      • Create a Mask
      • Dynamic shimming
    • Static B1+ shimming
      • Download test data
      • Start the GUI of Shimming Toolbox
      • Convert DICOM to NIfTI
      • Create a Mask
      • Static B1+ shimming: CV reduction
    • Shell scripts
      • demo_realtime_shimming.sh
      • B1+ shimming
    • Create B0 Coil Profiles
      • Download data
      • DICOM to NIFTI
      • Config file
      • Create the coil profiles
      • To create your own custom coil
  • Command Line Tools
    • Field mapping
      • st_prepare_fieldmap
      • st_unwrap
    • Shimming
      • st_b0shim
        • add-shim-coefs
        • convert-shim-coefs-format
        • dynamic
        • max-intensity
        • realtime-dynamic
      • st_b1shim
    • Masking
      • st_mask
        • bet
        • box
        • modify-binary-mask
        • mrs
        • rect
        • sct
        • softmask
        • sphere
        • threshold
    • File Conversion
      • st_dicom_to_nifti
    • Coil Profile Generation
      • st_create_coil_profiles
        • constraint-file
        • from-cad
        • from-field-maps
    • Image manipulation
      • st_image
        • concat
        • logical-and
      • st_maths
        • div
        • mag
        • mean
        • phase
        • std
    • Miscellaneous
      • st_download_data
      • st_sort_dicoms
    • System Tools
      • st_check_dependencies
      • st_dump_env_info
  • Help
  • FAQ
  • Citing Shimming Toolbox

Developer Section

  • Contributing to shimming-toolbox
    • Introduction
    • Opening an issue
      • Before Submitting a New Issue
      • Submitting an Issue
        • Issue Examples
    • Opening a Branch
    • Developing
      • Pre-commit checks
      • Conflicts
      • Code style
      • Documentation and docstrings
      • Testing
      • Licensing
    • Committing
      • Commit Titles
      • Commit Sequences
    • Submitting a Pull Request
      • PR Labels
      • Work in progress
      • Continuous Integration
      • Reviewers
      • Merging your PR
    • Versioning
  • Contributors
  • API Reference
    • Field mapping
      • complex_difference()
      • correct_2pi_offset()
      • get_mask()
      • prepare_fieldmap()
      • unwrap_phase()
      • prelude()
      • skimage_unwrap()
    • Masking
      • shape_cube()
      • shape_sphere()
      • shape_square()
      • shapes()
      • threshold()
      • modify_binary_mask()
      • resample_mask()
      • mask_mrs()
      • add_softmask_to_binmask()
      • create_gaussian_softmask()
      • create_linear_softmask()
      • create_softmask()
      • create_two_levels_softmask()
      • save_softmask()
    • Coils
      • Coil
        • Coil.dim
        • Coil.profile
        • Coil.affine
        • Coil.required_constraints
        • Coil.coef_sum_max
        • Coil.coef_channel_minmax
        • Coil.name
        • Coil.__init__()
        • Coil.load_constraints()
      • ScannerCoil
        • ScannerCoil.__init__()
      • get_scanner_constraints()
      • restrict_to_orders()
      • spherical_harmonics()
      • channels_per_order()
      • convert_spher_harm_to_dict()
      • ge_basis()
      • philips_basis()
      • reorder_to_manufacturer()
      • scaled_spher_harm()
      • sh_basis()
      • siemens_basis()
      • generate_meshgrid()
      • get_main_orientation()
      • phys_gradient()
      • phys_to_vox_coefs()
      • resample_from_to()
      • biot_savart()
      • generate_coil_bfield()
    • Shim
      • Sequencer
        • RealTimeSequencer
        • Sequencer
        • ShimSequencer
        • define_slices()
        • extend_fmap_to_kernel_size()
        • new_bounds_from_currents()
        • new_bounds_from_currents_static_to_riro()
        • parse_slices()
        • plot_full_mask()
        • shim_max_intensity()
      • Shim Utils
        • ScannerShimSettings
        • calculate_metric_within_mask()
        • convert_to_dac_units()
        • dac_to_shim_units()
        • extend_slice()
        • get_phase_encode_direction_sign()
        • phys_to_gradient_cs()
        • phys_to_shim_cs()
        • shim_to_phys_cs()
        • update_affine_for_ap_slices()
      • B1 Shim
        • b1shim()
        • combine_maps()
        • complex_to_vector()
        • load_siemens_vop()
        • max_sar()
        • phase_only_shimming()
        • vector_to_complex()
    • Optimizer
      • Optimizer
        • Optimizer.coils
        • Optimizer.unshimmed
        • Optimizer.unshimmed_affine
        • Optimizer.merged_coils
        • Optimizer.merged_bounds
        • Optimizer.mask_coefficients
        • Optimizer.__init__()
        • Optimizer.get_coil_mat_and_unshimmed()
        • Optimizer.merge_bounds()
        • Optimizer.merge_coils()
        • Optimizer.optimize()
        • Optimizer.set_merged_bounds()
        • Optimizer.set_unshimmed()
      • OptimizerUtils
        • OptimizerUtils.initial_guess_method
        • OptimizerUtils.initial_coefs
        • OptimizerUtils.reg_vector
        • OptimizerUtils.__init__()
        • OptimizerUtils.get_coil_mat_and_unshimmed()
        • OptimizerUtils.get_initial_guess()
        • OptimizerUtils.get_quadratic_term()
        • OptimizerUtils.merge_bounds()
        • OptimizerUtils.merge_coils()
        • OptimizerUtils.optimize()
        • OptimizerUtils.set_merged_bounds()
        • OptimizerUtils.set_unshimmed()
      • LsqOptimizer
        • LsqOptimizer.__init__()
        • LsqOptimizer.get_coil_mat_and_unshimmed()
        • LsqOptimizer.get_initial_guess()
        • LsqOptimizer.get_quadratic_term()
        • LsqOptimizer.get_quadratic_term_grad()
        • LsqOptimizer.merge_bounds()
        • LsqOptimizer.merge_coils()
        • LsqOptimizer.optimize()
        • LsqOptimizer.set_merged_bounds()
        • LsqOptimizer.set_unshimmed()
      • PmuLsqOptimizer
        • PmuLsqOptimizer.__init__()
        • PmuLsqOptimizer.define_rt_bounds()
        • PmuLsqOptimizer.get_coil_mat_and_unshimmed()
        • PmuLsqOptimizer.get_initial_guess()
        • PmuLsqOptimizer.get_quadratic_term()
        • PmuLsqOptimizer.get_quadratic_term_grad()
        • PmuLsqOptimizer.merge_bounds()
        • PmuLsqOptimizer.merge_coils()
        • PmuLsqOptimizer.optimize()
        • PmuLsqOptimizer.set_merged_bounds()
        • PmuLsqOptimizer.set_unshimmed()
      • PmuQuadProgOpt
        • PmuQuadProgOpt.__init__()
        • PmuQuadProgOpt.get_coil_mat_and_unshimmed()
        • PmuQuadProgOpt.get_cost_matrices()
        • PmuQuadProgOpt.get_initial_guess()
        • PmuQuadProgOpt.get_quadratic_term()
        • PmuQuadProgOpt.get_stability_factor()
        • PmuQuadProgOpt.merge_bounds()
        • PmuQuadProgOpt.merge_coils()
        • PmuQuadProgOpt.optimize()
        • PmuQuadProgOpt.set_merged_bounds()
        • PmuQuadProgOpt.set_unshimmed()
      • QuadProgOpt
        • QuadProgOpt.__init__()
        • QuadProgOpt.get_coil_mat_and_unshimmed()
        • QuadProgOpt.get_cost_matrices()
        • QuadProgOpt.get_initial_guess()
        • QuadProgOpt.get_quadratic_term()
        • QuadProgOpt.get_stability_factor()
        • QuadProgOpt.merge_bounds()
        • QuadProgOpt.merge_coils()
        • QuadProgOpt.optimize()
        • QuadProgOpt.set_merged_bounds()
        • QuadProgOpt.set_unshimmed()
      • BFGSOpt
        • BFGSOpt.__init__()
        • BFGSOpt.get_coil_mat_and_unshimmed()
        • BFGSOpt.get_initial_guess()
        • BFGSOpt.get_quadratic_term()
        • BFGSOpt.get_quadratic_term_grad()
        • BFGSOpt.merge_bounds()
        • BFGSOpt.merge_coils()
        • BFGSOpt.optimize()
        • BFGSOpt.set_merged_bounds()
        • BFGSOpt.set_unshimmed()
      • PmuBFGSOpt
        • PmuBFGSOpt.__init__()
        • PmuBFGSOpt.define_rt_bounds()
        • PmuBFGSOpt.get_coil_mat_and_unshimmed()
        • PmuBFGSOpt.get_initial_guess()
        • PmuBFGSOpt.get_quadratic_term()
        • PmuBFGSOpt.get_quadratic_term_grad()
        • PmuBFGSOpt.merge_bounds()
        • PmuBFGSOpt.merge_coils()
        • PmuBFGSOpt.optimize()
        • PmuBFGSOpt.set_merged_bounds()
        • PmuBFGSOpt.set_unshimmed()
    • Nifti file handling
      • NiftiFile
        • NiftiFile.__init__()
        • NiftiFile.get_filename()
        • NiftiFile.get_frequency()
        • NiftiFile.get_isocenter()
        • NiftiFile.get_json()
        • NiftiFile.get_json_info()
        • NiftiFile.get_manufacturers_model_name()
        • NiftiFile.get_path_nii()
        • NiftiFile.get_scanner_shim_settings()
        • NiftiFile.load_json()
        • NiftiFile.load_nii()
        • NiftiFile.save()
        • NiftiFile.set_nii()
      • safe_getter()
      • NiftiFieldMap
        • NiftiFieldMap.__init__()
        • NiftiFieldMap.extend_field_map()
        • NiftiFieldMap.extend_fmap_to_kernel_size()
        • NiftiFieldMap.get_filename()
        • NiftiFieldMap.get_frequency()
        • NiftiFieldMap.get_isocenter()
        • NiftiFieldMap.get_json()
        • NiftiFieldMap.get_json_info()
        • NiftiFieldMap.get_manufacturers_model_name()
        • NiftiFieldMap.get_path_nii()
        • NiftiFieldMap.get_scanner_shim_settings()
        • NiftiFieldMap.load_json()
        • NiftiFieldMap.load_nii()
        • NiftiFieldMap.save()
        • NiftiFieldMap.set_nii()
      • NiftiMask
        • NiftiMask.__init__()
        • NiftiMask.get_filename()
        • NiftiMask.get_frequency()
        • NiftiMask.get_isocenter()
        • NiftiMask.get_json()
        • NiftiMask.get_json_info()
        • NiftiMask.get_manufacturers_model_name()
        • NiftiMask.get_path_nii()
        • NiftiMask.get_scanner_shim_settings()
        • NiftiMask.load_json()
        • NiftiMask.load_mask()
        • NiftiMask.load_nii()
        • NiftiMask.save()
        • NiftiMask.set_nii()
      • NiftiTarget
        • NiftiTarget.__init__()
        • NiftiTarget.get_fat_sat_option()
        • NiftiTarget.get_filename()
        • NiftiTarget.get_frequency()
        • NiftiTarget.get_isocenter()
        • NiftiTarget.get_json()
        • NiftiTarget.get_json_info()
        • NiftiTarget.get_manufacturers_model_name()
        • NiftiTarget.get_path_nii()
        • NiftiTarget.get_scanner_shim_settings()
        • NiftiTarget.load_json()
        • NiftiTarget.load_nii()
        • NiftiTarget.save()
        • NiftiTarget.set_nii()
    • Image manipulation
      • concat_data()
    • Numerical model
      • NumericalModel
        • NumericalModel.gamma
        • NumericalModel.field_strength
        • NumericalModel.handedness
        • NumericalModel.measurement
        • NumericalModel.proton_density
        • NumericalModel.T2_star
        • NumericalModel.generate_deltaB0()
        • NumericalModel.save()
        • NumericalModel.simulate_measurement()
    • Miscellaneous
      • Dicom to Nifti
        • dicom_to_nifti()
        • fix_tfl_b1()
      • Load Nifti
        • get_acquisition_times()
        • load_nifti()
        • read_nii()
      • Download
        • download_data()
        • install_data()
        • unzip()
      • PMU
        • PmuResp
      • Shimming toolbox utils
        • add_suffix()
        • check_exe()
        • create_fname_from_path()
        • create_output_dir()
        • fill()
        • iso_times_to_ms()
        • montage()
        • run_subprocess()
        • save_nii_json()
        • set_all_loggers()
        • splitext()
        • st_progress_bar()
        • timeit()
  • Changelog
    • 1.3 (2025-07-29)
      • PACKAGE: SHIMMING TOOLBOX
      • PACKAGE: PLUGIN
      • REPO
    • 1.2 (2025-03-31)
      • PACKAGE: SHIMMING TOOLBOX
      • PACKAGE: PLUGIN
      • REPO
    • 1.1 (2024-11-08)
      • PACKAGE: SHIMMING TOOLBOX
      • REPO
    • 1.0 (2024-08-21)
      • PACKAGE: SHIMMING TOOLBOX
      • PACKAGE: PLUGIN
      • REPO
    • 0.1 (2021-07-28)
      • PACKAGE: SHIMMING TOOLBOX
      • PACKAGE: PLUGIN
      • REPO

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