Overview
User Section
Developer Section
complex_difference()
correct_2pi_offset()
get_mask()
prepare_fieldmap()
unwrap_phase()
prelude()
shape_cube()
shape_sphere()
shape_square()
shapes()
threshold()
modify_binary_mask()
resample_mask()
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()
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.extended_fmap
RealTimeSequencer.eval()
RealTimeSequencer.get_acq_pressures()
RealTimeSequencer.get_fieldmap()
RealTimeSequencer.get_real_time_parameters()
RealTimeSequencer.load_masks()
RealTimeSequencer.optimize_riro()
RealTimeSequencer.plot_currents()
RealTimeSequencer.plot_full_time_std()
RealTimeSequencer.plot_pressure_and_unshimmed_field()
RealTimeSequencer.plot_pressure_vs_field()
RealTimeSequencer.plot_shimmed_trace()
RealTimeSequencer.print_rt_metrics()
RealTimeSequencer.resample_mask_to_target()
RealTimeSequencer.resample_masks_to_target_per_shim()
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.calc_shimmed_gradient_full_mask()
ShimSequencer.display_shimmed_results()
ShimSequencer.eval()
ShimSequencer.evaluate_shimming()
ShimSequencer.get_anat()
ShimSequencer.get_fieldmap()
ShimSequencer.get_resampled_masks()
ShimSequencer.load_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()
new_bounds_from_currents_static_to_riro()
parse_slices()
plot_full_mask()
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.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.define_rt_bounds()
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()
concat_data()
NumericalModel
NumericalModel.gamma
NumericalModel.field_strength
NumericalModel.handedness
NumericalModel.measurement
NumericalModel.proton_density
NumericalModel.T2_star
NumericalModel.generate_deltaB0()
NumericalModel.save()
NumericalModel.simulate_measurement()
dicom_to_nifti()
fix_tfl_b1()
get_isocenter()
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.adjust_start_time()
PmuResp.get_all_times()
PmuResp.get_data()
PmuResp.get_mean_trigger_span()
PmuResp.get_pressure_rms()
PmuResp.get_resp_trace()
PmuResp.get_start_and_stop_times()
PmuResp.get_times()
PmuResp.get_trigger_times()
PmuResp.interp_resp_trace()
PmuResp.mean()
PmuResp.read_resp()
PmuResp.set_data()
PmuResp.set_start_and_stop_times()
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()
About
We provide the following hands-on tutorials to get familiar with the GUI and the command line tools.