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
      • 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
    • Shimming
      • st_b0shim
        • dynamic
        • gradient-realtime
        • max-intensity
        • realtime-dynamic
      • st_b1shim
    • Masking
      • st_mask
        • box
        • rect
        • sct
        • sphere
        • threshold
    • File Conversion
      • st_dicom_to_nifti
    • Coil Profile Generation
      • st_create_coil_profiles
        • from-cad
        • from-field-maps
    • Image manipulation
      • st_image
        • concat
        • logical-and
      • st_maths
        • mean
    • Miscellaneous
      • st_download_data
    • System Tools
      • st_check_dependencies
      • st_dump_env_info
  • Help
  • 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
    • Fieldmapping
      • complex_difference()
      • correct_2pi_offset()
      • prepare_fieldmap()
      • unwrap_phase()
      • prelude()
    • Masking
      • shape_cube()
      • shape_sphere()
      • shape_square()
      • shapes()
      • threshold()
      • dilate_binary_mask()
      • resample_mask()
    • 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_sph_constraints()
      • spherical_harmonics()
      • ge_basis()
      • get_flip_matrix()
      • scaled_spher_harm()
      • siemens_basis()
      • generate_meshgrid()
      • get_main_orientation()
      • phys_gradient()
      • phys_to_vox_coefs()
      • resample_from_to()
      • biot_savart()
      • generate_coil_bfield()
    • Shim
      • realtime_shim()
      • RealTimeSequencer
        • RealTimeSequencer.nii_fieldmap
        • RealTimeSequencer.json_fmap
        • RealTimeSequencer.nii_anat
        • RealTimeSequencer.nii_static_mask
        • RealTimeSequencer.nii_riro_mask
        • RealTimeSequencer.slices
        • RealTimeSequencer.pmu
        • RealTimeSequencer.coils
        • RealTimeSequencer.method
        • RealTimeSequencer.opt_criteria
        • RealTimeSequencer.reg_factor
        • RealTimeSequencer.mask_dilation_kernel
        • RealTimeSequencer.mask_dilation_kernel_size
        • RealTimeSequencer.path_output
        • RealTimeSequencer.optimizer
        • RealTimeSequencer.optimizer_riro
        • RealTimeSequencer.bounds
        • RealTimeSequencer.acq_pressures
        • RealTimeSequencer.acq_timestamps
        • RealTimeSequencer.eval()
        • RealTimeSequencer.get_acq_pressures()
        • RealTimeSequencer.get_fieldmap()
        • RealTimeSequencer.get_mask()
        • RealTimeSequencer.get_real_time_parameters()
        • RealTimeSequencer.get_riro_and_static_resampled_masks()
        • RealTimeSequencer.optimize_riro()
        • RealTimeSequencer.plot_currents()
        • RealTimeSequencer.plot_full_mask()
        • RealTimeSequencer.plot_full_time_std()
        • RealTimeSequencer.plot_pressure_and_unshimmed_field()
        • RealTimeSequencer.plot_shimmed_trace()
        • RealTimeSequencer.plot_static_riro()
        • RealTimeSequencer.print_rt_metrics()
        • RealTimeSequencer.select_optimizer()
        • RealTimeSequencer.shim()
      • Sequencer
        • Sequencer.slices
        • Sequencer.mask_dilation_kernel
        • Sequencer.mask_dilation_kernel_size
        • Sequencer.reg_factor
        • Sequencer.path_output
        • Sequencer.index_shimmed
        • Sequencer.index_not_shimmed
        • Sequencer.optimize()
      • ShimSequencer
        • ShimSequencer.nii_fieldmap
        • ShimSequencer.nii_anat
        • ShimSequencer.nii_mask_anat
        • ShimSequencer.coils
        • ShimSequencer.method
        • ShimSequencer.opt_criteria
        • ShimSequencer.nii_fieldmap_orig
        • ShimSequencer.optimizer
        • ShimSequencer.fmap_is_extended
        • ShimSequencer.masks_fmap
        • ShimSequencer.calc_shimmed_anat_orient()
        • ShimSequencer.calc_shimmed_full_mask()
        • ShimSequencer.display_shimmed_results()
        • ShimSequencer.eval()
        • ShimSequencer.evaluate_shimming()
        • ShimSequencer.get_anat()
        • ShimSequencer.get_fieldmap()
        • ShimSequencer.get_mask()
        • ShimSequencer.get_resampled_masks()
        • ShimSequencer.plot_currents()
        • ShimSequencer.plot_full_mask()
        • ShimSequencer.plot_partial_mask()
        • ShimSequencer.select_optimizer()
        • ShimSequencer.shim()
      • define_slices()
      • extend_fmap_to_kernel_size()
      • extend_slice()
      • new_bounds_from_currents()
      • parse_slices()
      • shim_max_intensity()
      • update_affine_for_ap_slices()
      • 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.__init__()
        • Optimizer.get_coil_mat_and_unshimmed()
        • Optimizer.merge_bounds()
        • Optimizer.merge_coils()
        • Optimizer.optimize()
        • Optimizer.set_merged_bounds()
        • Optimizer.set_unshimmed()
      • LsqOptimizer
        • LsqOptimizer.__init__()
        • LsqOptimizer.get_coil_mat_and_unshimmed()
        • LsqOptimizer.get_initial_guess()
        • LsqOptimizer.get_quadratic_term()
        • LsqOptimizer.merge_bounds()
        • LsqOptimizer.merge_coils()
        • LsqOptimizer.optimize()
        • LsqOptimizer.set_merged_bounds()
        • LsqOptimizer.set_unshimmed()
      • PmuLsqOptimizer
        • PmuLsqOptimizer.__init__()
        • PmuLsqOptimizer.get_coil_mat_and_unshimmed()
        • PmuLsqOptimizer.get_initial_guess()
        • PmuLsqOptimizer.get_quadratic_term()
        • PmuLsqOptimizer.merge_bounds()
        • PmuLsqOptimizer.merge_coils()
        • PmuLsqOptimizer.optimize()
        • PmuLsqOptimizer.set_merged_bounds()
        • PmuLsqOptimizer.set_unshimmed()
    • 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()
      • fix_tfl_b1()
      • get_acquisition_times()
      • load_nifti()
      • read_nii()
      • download_data()
      • install_data()
      • unzip()
      • PmuResp
        • PmuResp.fname
        • PmuResp.data
        • PmuResp.start_time_mdh
        • PmuResp.stop_time_mdh
        • PmuResp.start_time_mpcu
        • PmuResp.stop_time_mpcu
        • PmuResp.get_times()
        • PmuResp.interp_resp_trace()
        • PmuResp.read_resp()
      • add_suffix()
      • 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()

About

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  • Edit on GitHub

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© Copyright 2020, NeuroPoly Lab, Polytechnique Montreal. Revision c9975f7d.

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