├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── pythonpackage.yml │ └── pythonpackage_dev.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── KNOWN_ISSUES.md ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── VERSION ├── _build ├── .buildinfo ├── .doctrees │ ├── docs │ │ └── source │ │ │ ├── modules.doctree │ │ │ ├── virtualscanner.coms.coms_ui.doctree │ │ │ ├── virtualscanner.coms.doctree │ │ │ ├── virtualscanner.doctree │ │ │ ├── virtualscanner.server.ana.doctree │ │ │ ├── virtualscanner.server.doctree │ │ │ ├── virtualscanner.server.recon.doctree │ │ │ ├── virtualscanner.server.recon.drunck.doctree │ │ │ ├── virtualscanner.server.registration.doctree │ │ │ ├── virtualscanner.server.rf.doctree │ │ │ ├── virtualscanner.server.rf.rx.doctree │ │ │ ├── virtualscanner.server.rf.tx.SAR_calc.doctree │ │ │ ├── virtualscanner.server.rf.tx.doctree │ │ │ ├── virtualscanner.server.simulation.bloch.doctree │ │ │ ├── virtualscanner.server.simulation.doctree │ │ │ └── virtualscanner.utils.doctree │ ├── environment.pickle │ └── index.doctree ├── _images │ └── virtual_scanner_logo_v1.png ├── _sources │ ├── docs │ │ └── source │ │ │ ├── modules.rst.txt │ │ │ ├── virtualscanner.coms.coms_ui.rst.txt │ │ │ ├── virtualscanner.coms.rst.txt │ │ │ ├── virtualscanner.rst.txt │ │ │ ├── virtualscanner.server.ana.rst.txt │ │ │ ├── virtualscanner.server.recon.drunck.rst.txt │ │ │ ├── virtualscanner.server.recon.rst.txt │ │ │ ├── virtualscanner.server.registration.rst.txt │ │ │ ├── virtualscanner.server.rf.rst.txt │ │ │ ├── virtualscanner.server.rf.rx.rst.txt │ │ │ ├── virtualscanner.server.rf.tx.SAR_calc.rst.txt │ │ │ ├── virtualscanner.server.rf.tx.rst.txt │ │ │ ├── virtualscanner.server.rst.txt │ │ │ ├── virtualscanner.server.simulation.bloch.rst.txt │ │ │ ├── virtualscanner.server.simulation.rst.txt │ │ │ └── virtualscanner.utils.rst.txt │ └── index.rst.txt ├── _static │ ├── basic.css │ ├── classic.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── jquery-3.2.1.js │ ├── jquery.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── sidebar.js │ ├── underscore-1.3.1.js │ └── underscore.js ├── docs │ └── source │ │ ├── modules.html │ │ ├── virtualscanner.coms.coms_ui.html │ │ ├── virtualscanner.coms.html │ │ ├── virtualscanner.html │ │ ├── virtualscanner.server.ana.html │ │ ├── virtualscanner.server.html │ │ ├── virtualscanner.server.recon.drunck.html │ │ ├── virtualscanner.server.recon.html │ │ ├── virtualscanner.server.registration.html │ │ ├── virtualscanner.server.rf.html │ │ ├── virtualscanner.server.rf.rx.html │ │ ├── virtualscanner.server.rf.tx.SAR_calc.html │ │ ├── virtualscanner.server.rf.tx.html │ │ ├── virtualscanner.server.simulation.bloch.html │ │ ├── virtualscanner.server.simulation.html │ │ └── virtualscanner.utils.html ├── genindex.html ├── index.html ├── objects.inv ├── py-modindex.html ├── search.html └── searchindex.js ├── conf.py ├── docs └── source │ ├── modules.rst │ ├── virtualscanner.coms.coms_ui.rst │ ├── virtualscanner.coms.rst │ ├── virtualscanner.rst │ ├── virtualscanner.server.ana.rst │ ├── virtualscanner.server.recon.drunck.rst │ ├── virtualscanner.server.recon.rst │ ├── virtualscanner.server.registration.rst │ ├── virtualscanner.server.rf.rst │ ├── virtualscanner.server.rf.rx.rst │ ├── virtualscanner.server.rf.tx.SAR_calc.rst │ ├── virtualscanner.server.rf.tx.rst │ ├── virtualscanner.server.rst │ ├── virtualscanner.server.simulation.bloch.rst │ ├── virtualscanner.server.simulation.rst │ └── virtualscanner.utils.rst ├── index.rst ├── make.bat ├── paper ├── paper.bib └── paper.md ├── pull_request_template.md ├── requirements.txt ├── setup.py ├── sphinx-apidoc └── virtualscanner ├── __init__.py ├── coms ├── __init__.py └── coms_ui │ ├── GUI_test_functions.py │ ├── GUI_utest.py │ ├── __init__.py │ ├── coms_server_flask.py │ ├── firefox_driver │ ├── geckodriver_mac │ └── geckodriver_windows.exe │ ├── standard_mode_GUI_selenium.py │ ├── static │ ├── RF │ │ ├── Rx │ │ │ └── inputs │ │ │ │ ├── axial.png │ │ │ │ ├── coronal.png │ │ │ │ └── sagittal.png │ │ └── Tx │ │ │ └── SAR │ │ │ └── SAR1.png │ ├── __init__.py │ ├── acquire_func.js │ ├── acquire_style.css │ ├── advanced │ │ ├── Rx.png │ │ ├── Tx.png │ │ ├── computer.png │ │ ├── gradients.png │ │ └── human-form.png │ ├── advanced_mode_style.css │ ├── ana │ │ ├── inputs │ │ │ ├── T1_original_data │ │ │ │ ├── T1_experiments_data_1.png │ │ │ │ ├── T1_experiments_data_2.png │ │ │ │ ├── T1_experiments_data_3.png │ │ │ │ ├── T1_experiments_data_4.png │ │ │ │ ├── T1_experiments_data_5.png │ │ │ │ ├── T1_experiments_data_6.png │ │ │ │ └── T1_experiments_data_7.png │ │ │ └── T2_original_data │ │ │ │ ├── T2_experiments_data_1.png │ │ │ │ ├── T2_experiments_data_2.png │ │ │ │ ├── T2_experiments_data_3.png │ │ │ │ ├── T2_experiments_data_4.png │ │ │ │ ├── T2_experiments_data_5.png │ │ │ │ ├── T2_experiments_data_6.png │ │ │ │ └── T2_experiments_data_7.png │ │ └── outputs │ │ │ └── pat_id │ │ │ ├── T1_map.dcm │ │ │ └── T2_map.dcm │ ├── analyze_func.js │ ├── analyze_style.css │ ├── favicomatic │ │ ├── code.txt │ │ ├── favicon-16x16.png │ │ └── favicon-32x32.png │ ├── favicon.ico │ ├── form2Json.js │ ├── log_in_func.js │ ├── log_in_style.css │ ├── log_out_func.js │ ├── logo-blue-white-onlycrown.png │ ├── main_style.css │ ├── metric_imperial.js │ ├── packages │ │ ├── Bootstrap │ │ │ ├── bootstrap.min.css │ │ │ ├── bootstrap.min.js │ │ │ ├── jquery-3.3.1.slim.min.js │ │ │ └── popper.min.js │ │ ├── jQuery-ui │ │ │ ├── jquery-ui.css │ │ │ └── jquery-ui.js │ │ └── jquery-3.3.1.min.js │ ├── phantomAutofill.js │ ├── phantom_pics │ │ ├── ISMRM-NIST.jpg │ │ ├── Numerical.png │ │ └── PHOTO BY ME.jpg │ ├── recon │ │ ├── __init__.py │ │ └── recon_example.png │ ├── recon_func.js │ ├── recon_style.css │ ├── register_func.js │ ├── register_style.css │ ├── rx_func.js │ ├── rx_style.css │ ├── screenshots │ │ ├── acquire.JPG │ │ ├── analyze.JPG │ │ ├── notes.txt │ │ ├── register.JPG │ │ ├── rx.png │ │ └── tx.JPG │ ├── tx_func.js │ ├── tx_style.css │ ├── user_uploads │ │ └── test_notvalid.jpg │ └── virtual_scanner_logo_v1.png │ ├── templates │ ├── acquire.html │ ├── analyze.html │ ├── log_in.html │ ├── recon.html │ ├── register.html │ ├── rx.html │ └── tx.html │ └── utest_coms_ui.py ├── notebooks ├── Virtual Scanner 2.0 - B0 and B1 map simulation demo - 2022 updated.ipynb ├── Virtual Scanner 2.0 - RF simulation - 2022 updated.ipynb ├── Virtual Scanner 2.0 Demo - 2022 updated.ipynb ├── Virtual_Scanner_2_0_MRpub_submission.ipynb ├── data │ ├── b0_map_smaller_Hz.mat │ ├── epi_pypulseq_32.seq │ └── rx_maps_ds_16_32.mat └── py2jemris_demo.ipynb ├── server ├── __init__.py ├── ana │ ├── ROI_analysis.py │ ├── T1_mapping.py │ ├── T2_mapping.py │ ├── __init__.py │ ├── inputs │ │ ├── T1_map_mac │ │ │ ├── utest_T1_map.dcm │ │ │ ├── utest_T1_map.npy │ │ │ ├── utest_T1_map.png │ │ │ └── utest_T1_map_with_ROI.png │ │ ├── T1_map_windows │ │ │ ├── utest_T1_map.dcm │ │ │ ├── utest_T1_map.npy │ │ │ ├── utest_T1_map.png │ │ │ └── utest_T1_map_with_ROI.png │ │ ├── T1_orig_data │ │ │ ├── 1_T1_exp_TI_21.dcm │ │ │ ├── 2_T1_exp_TI_100.dcm │ │ │ ├── 3_T1_exp_TI_200.dcm │ │ │ ├── 4_T1_exp_TI_400.dcm │ │ │ ├── 5_T1_exp_TI_800.dcm │ │ │ ├── 6_T1_exp_TI_1600.dcm │ │ │ └── 7_T1_exp_TI_3200.dcm │ │ ├── T2_map_mac │ │ │ ├── utest_T2_map.dcm │ │ │ ├── utest_T2_map.npy │ │ │ ├── utest_T2_map.png │ │ │ └── utest_T2_map_with_ROI.png │ │ ├── T2_map_windows │ │ │ ├── utest_T2_map.dcm │ │ │ ├── utest_T2_map.npy │ │ │ ├── utest_T2_map.png │ │ │ └── utest_T2_map_with_ROI.png │ │ └── T2_orig_data │ │ │ ├── 01_T2_exp_TE_12.dcm │ │ │ ├── 02_T2_exp_TE_22.dcm │ │ │ ├── 03_T2_exp_TE_42.dcm │ │ │ ├── 04_T2_exp_TE_62.dcm │ │ │ ├── 05_T2_exp_TE_102.dcm │ │ │ ├── 06_T2_exp_TE_152.dcm │ │ │ ├── 07_T2_exp_TE_202.dcm │ │ │ ├── 08_T2_exp_TE_12.dcm │ │ │ ├── 09_T2_exp_TE_15.dcm │ │ │ ├── 10_T2_exp_TE_18.dcm │ │ │ └── 11_T2_exp_TE_21.dcm │ ├── outputs │ │ ├── 1402 │ │ │ └── T1_map │ │ │ │ └── T1_map20190823153715.dcm │ │ ├── T1_map │ │ │ └── T1_map.dcm │ │ └── T2_map │ │ │ └── T2_map.dcm │ ├── utest_ROI_analysis_T1_T2.py │ └── utest_T1_T2_mapping.py ├── recon │ ├── __init__.py │ ├── drunck │ │ ├── __init__.py │ │ ├── assets │ │ │ ├── model.hdf5 │ │ │ ├── utest_recon.jpg │ │ │ └── utest_undersampled.jpg │ │ ├── nifti2npy.py │ │ ├── reconstruct.py │ │ └── utest_reconstruct.py │ ├── non-Cartesian │ │ └── README.txt │ └── radial_ktraj.mat ├── registration │ ├── __init__.py │ ├── db_operations_mgr.py │ ├── register.py │ ├── subject.db │ └── utest_register.py ├── rf │ ├── __init__.py │ ├── rx │ │ ├── __init__.py │ │ ├── axial.png │ │ ├── caller_script_Rx.py │ │ ├── coronal.png │ │ └── sagittal.png │ └── tx │ │ ├── SAR_calc │ │ ├── SAR_calc_main.py │ │ ├── __init__.py │ │ ├── assets │ │ │ ├── QGlobal.mat │ │ │ └── rad2d.seq │ │ └── utest_SAR_calc.py │ │ └── __init__.py └── simulation │ ├── __init__.py │ ├── bloch │ ├── __init__.py │ ├── attempt_new_solver.py │ ├── caller_script_blochsim.py │ ├── db0_sim_signal_t1plane_tse_testv2.mat │ ├── demo │ │ ├── tse_ms_FOV250mm_N16_Ns1_TR3000ms_TE50ms_4echoes_dwell400.0us.seq │ │ ├── tse_pe_info.mat │ │ └── tse_phase_info.mat │ ├── irse.seq │ ├── irse_info.mat │ ├── pe_info.mat │ ├── phantom.py │ ├── phantom_acr.py │ ├── pulseq_bloch_simulator.py │ ├── pulseq_blochsim_methods.py │ ├── pulseq_library.py │ ├── pulseq_library_v2.py │ ├── script_bloch_pulseq.py │ ├── script_bloch_pulseq_epi.py │ ├── script_bloch_pulseq_sim_v2.py │ ├── sim │ │ ├── __init__.py │ │ ├── amri_debug │ │ │ ├── b0demo │ │ │ │ ├── B0_map_demo_phantom.png │ │ │ │ ├── b0_sim_5x.png │ │ │ │ ├── b0_sim_figure.png │ │ │ │ ├── b0map_corr.mat │ │ │ │ ├── b0sim_brainweb32_tse_zero_df.mat │ │ │ │ ├── brainweb.mat │ │ │ │ ├── brainweb.npy │ │ │ │ ├── brainweb_sim_source_data_32.mat │ │ │ │ ├── bw_params.mat │ │ │ │ ├── db0_sim_signal_bw_tse_nodf_default_rf.mat │ │ │ │ ├── db0_sim_signal_bw_tse_withdf_5x_default_rf.mat │ │ │ │ ├── db0_sim_signal_bw_tse_withdf_default_rf.mat │ │ │ │ ├── db0_sim_signal_t1plane_tse_nodf.mat │ │ │ │ ├── db0_sim_signal_t1plane_tse_withdf.mat │ │ │ │ ├── match_brainweb_phantom.m │ │ │ │ ├── phantom_figure.png │ │ │ │ ├── show_b0_sim.py │ │ │ │ ├── tse_ms_FOV250mm_N32_Ns1_TR2000ms_TE12ms_4echoes_dwell200.0us.seq │ │ │ │ └── tse_pe_info.mat │ │ │ ├── cylindrical_upload_test.mat │ │ │ ├── mprage3d │ │ │ │ ├── 3d_t1_mprage_pypulseq.seq │ │ │ │ ├── 3d_t1_mprage_pypulseq_Nx16Ny16Nz1.seq │ │ │ │ ├── n16_show.PNG │ │ │ │ ├── sim_debug_mprage_061621.py │ │ │ │ ├── simulated_signal.mat │ │ │ │ └── write_3Dt1_mprage.py │ │ │ ├── simseqs │ │ │ │ ├── flair_ms_FOV240mm_N32_Ns1_TR10000ms_TE13ms_TI2600ms.seq │ │ │ │ ├── flair_new │ │ │ │ │ ├── flair_fast_ms_FOV240mm_N32_Ns1_TR10000ms_TE13ms_TI2600ms.seq │ │ │ │ │ ├── flair_fast_pe_order.mat │ │ │ │ │ └── flair_new_signal.mat │ │ │ │ ├── flair_pe_order.mat │ │ │ │ ├── flair_sim_32_T1plane.png │ │ │ │ ├── flair_sim_32_T2plane_new.png │ │ │ │ ├── sim_seqs_amri.py │ │ │ │ ├── simed_images.mat │ │ │ │ ├── simulated_signal_FLAIR.mat │ │ │ │ ├── simulated_signal_tse.mat │ │ │ │ ├── tse_ms_FOV250mm_N32_Ns1_TR2000ms_TE12ms_4echoes_dwell200.0us.seq │ │ │ │ ├── tse_pe_info.mat │ │ │ │ └── tse_sim_32_t2plane.png │ │ │ └── spgr │ │ │ │ ├── adc_phase_test_spgr_rfspoil_sim.py │ │ │ │ ├── debug_spgr.m │ │ │ │ ├── sim_debug_spgr_060121.py │ │ │ │ ├── spgr_gspoil_debug.seq │ │ │ │ ├── spgr_rf_phases_16_20210526.mat │ │ │ │ ├── spgr_rfspoil_adc_phase_test.mat │ │ │ │ ├── spgr_rfspoil_mmj.seq │ │ │ │ └── stored_sim_magnetizations.mat │ │ ├── dwi_simple_sim │ │ │ ├── DWI_pypulseq_colab.seq │ │ │ ├── DWI_pypulseq_colab_N16_Nb1_Ndir6_thk5.seq │ │ │ ├── b_val.mat │ │ │ ├── dwi_sim_try.mat │ │ │ ├── dwi_sim_try_default-sg.mat │ │ │ ├── outcome.png │ │ │ ├── outcome_default_sim.png │ │ │ ├── outcome_updated.png │ │ │ └── show_dwi_sim.py │ │ ├── minTE_bloch_simulations │ │ │ ├── ADC2_swift_FA5_N16.seq │ │ │ ├── CODE_dcf_ktraj_voronoi.mat │ │ │ ├── __init__.py │ │ │ ├── code_TR100_TE0.16_FA15_N16.seq │ │ │ ├── code_signal.mat │ │ │ ├── ktraj_code_TR100_TE0.16_FA15_N16.mat │ │ │ ├── minTE_bloch_simulations.py │ │ │ ├── minTE_test_point_phantom.mat │ │ │ ├── swift_info_FA5_N16.mat │ │ │ └── swift_signal.mat │ │ ├── seq_validation_bloch_simulations.py │ │ ├── seq_validation_files │ │ │ ├── IRSE32_4spheres_blochsim.png │ │ │ ├── TSE32_4spheres_blochsim.png │ │ │ ├── april_log.txt │ │ │ ├── gen_bloch_sim_figures.m │ │ │ ├── irse32.seq │ │ │ ├── irse32_debug.mat │ │ │ ├── irse32_readout_fixed_T1plane32.mat │ │ │ ├── irse64.seq │ │ │ ├── irse64_grid128.mat │ │ │ ├── march_log.txt │ │ │ ├── pe_info.mat │ │ │ ├── phantom.h5 │ │ │ ├── phantom_stored │ │ │ │ ├── T1plane.mat │ │ │ │ ├── T2plane.mat │ │ │ │ ├── disp_pht.m │ │ │ │ ├── grid.mat │ │ │ │ ├── phantom.h5 │ │ │ │ ├── phantom_fig.png │ │ │ │ ├── pht0420.h5 │ │ │ │ └── pht0420_2.h5 │ │ │ ├── simulated │ │ │ │ ├── irse │ │ │ │ │ ├── irse32_signal_acr.mat │ │ │ │ │ ├── irse32_signal_acr2.mat │ │ │ │ │ └── irse32_signal_cylindrical.mat │ │ │ │ ├── irse32_signal_grid0420_solver.mat │ │ │ │ ├── irse32_signal_planeT1_spheresN128.mat │ │ │ │ ├── isc_signal.mat │ │ │ │ ├── isc_signal_4xT2.mat │ │ │ │ ├── isc_signal_cancel-2-ADC.mat │ │ │ │ ├── isc_signal_cancel-2-ADC_new.mat │ │ │ │ ├── isc_signal_doubleT1.mat │ │ │ │ ├── starting_k0_tse_pe_info.mat │ │ │ │ ├── tse │ │ │ │ │ ├── pe_info.mat │ │ │ │ │ └── tse32_signal_cylindrical.mat │ │ │ │ ├── tse32_k0_signal_4spheres_N32_solver.mat │ │ │ │ ├── tse32_signal_acr.mat │ │ │ │ ├── tse32_signal_acr2.mat │ │ │ │ ├── tse32_signal_grid0420_solver.mat │ │ │ │ ├── tse32_signal_planeT1_spheresN128.mat │ │ │ │ ├── tse32_signal_planeT1_spheresN32_solver.mat │ │ │ │ ├── tse32_signal_planeT2_spheresN128.mat │ │ │ │ ├── tse32_starting_k0.seq │ │ │ │ ├── tse32_zero.seq │ │ │ │ ├── tse32_zero_circle.mat │ │ │ │ ├── tse32_zero_circle_longerT2-250.mat │ │ │ │ ├── tse64_signal_T1plane128_solver.mat │ │ │ │ └── tse64_signal_grid0420_N128_solver.mat │ │ │ ├── tse32.seq │ │ │ ├── tse32_T2plane.mat │ │ │ ├── tse32_grid32.mat │ │ │ ├── tse32_grid64.mat │ │ │ ├── tse32_readout_fixed_T1plane32.mat │ │ │ ├── tse64.seq │ │ │ ├── tse64_grid128.mat │ │ │ └── tse64_grid128_ro_fixed.mat │ │ ├── single_isochromat_test_tse.py │ │ └── vs2.0_fig2 │ │ │ ├── my_phantom.mat │ │ │ ├── signal_spgr_no_adc_phase_T1.mat │ │ │ ├── signal_spgr_with_adc_phase_T1.mat │ │ │ ├── signal_spgr_with_adc_phase_T1_opp_phase.mat │ │ │ ├── simulate_32.py │ │ │ ├── spgr_sim_110221_no_adc_phase.seq │ │ │ └── spgr_sim_110221_with_adc_phase.seq │ ├── spingroup_ps.py │ ├── spingroup_ps_wsolver.py │ ├── test_data │ │ └── test_cylindrical_phantom_maps.npy │ ├── test_pht2h5.py │ ├── tse.seq │ ├── tse_info.mat │ ├── utest_bloch_pulseq.py │ ├── utest_bloch_pulseq_epi.py │ ├── utest_phantoms.py │ ├── utest_pulseq_library.py │ ├── utest_spingroup.py │ ├── util.py │ ├── write_irse_interleaved_split_grad.py │ └── write_tse.py │ ├── epi_pypulseq.seq │ ├── oblique.seq │ ├── pulseq_signal_new.npy │ ├── py2jemris │ ├── benchmark_seq2xml │ │ ├── .jemris_progress.out │ │ ├── .spins_state.dat │ │ ├── benchmark_seq_files.py │ │ ├── ext_rf.h5 │ │ ├── gre.h5 │ │ ├── gre.xml │ │ ├── gre_jemris.seq │ │ ├── gre_jemris_seq2xml.xml │ │ ├── gre_jemris_seq2xml_jemris.h5 │ │ ├── gre_jemris_seq2xml_jemris.seq │ │ ├── mysimu2.xml │ │ ├── rf_1.h5 │ │ ├── rf_2.h5 │ │ ├── rf_3.h5 │ │ ├── rf_4.h5 │ │ ├── rf_5.h5 │ │ ├── rf_6.h5 │ │ ├── rf_7.h5 │ │ ├── rf_8.h5 │ │ ├── sample.h5 │ │ ├── seq_compare.PNG │ │ ├── seq_compare_zoomed.PNG │ │ ├── signals.h5 │ │ └── uniform.xml │ ├── coil2xml.py │ ├── examine_seq_diag.py │ ├── make_some_seqs.py │ ├── orc_test │ │ ├── __init__.py │ │ └── plot_orc_sequence.py │ ├── pulseq_jemris_simulator.py │ ├── recon_jemris.py │ ├── sample.h5 │ ├── seq2xml.py │ ├── seq_files │ │ ├── FLASH_N256_Ns16_TE5ms_TR10ms_FA8deg.seq │ │ ├── myseq.seq │ │ ├── signals.h5 │ │ ├── spgr_gspoil_N16_Ns1_TE5ms_TR10ms_FA30deg.seq │ │ └── system_parameters.txt │ ├── sim │ │ ├── 8chheadcyl.xml │ │ ├── __init__.py │ │ ├── epi.xml │ │ ├── gre.xml │ │ ├── sample.h5 │ │ ├── test0501 │ │ │ └── uniform.xml │ │ ├── testfolder │ │ │ ├── sample_100101102.h5 │ │ │ └── uniform.xml │ │ ├── tse.xml │ │ ├── uniform.xml │ │ └── utest_outputs │ │ │ ├── .jemris_progress.out │ │ │ ├── cylindrical.h5 │ │ │ ├── data32_orig.mat │ │ │ ├── gre32.xml │ │ │ ├── signals.h5 │ │ │ ├── simu.xml │ │ │ └── uniform.xml │ ├── sim2xml.py │ ├── sim_jemris.py │ ├── try_seq2xml │ │ ├── .jemris_progress.out │ │ ├── MySimu.xml │ │ ├── example.xml │ │ ├── log.txt │ │ ├── outputs │ │ │ └── Figure_1.png │ │ ├── rf_1.h5 │ │ ├── sample.h5 │ │ ├── signals.h5 │ │ ├── spgr_gspoil_N15_Ns1_TE5ms_TR10ms_FA30deg.seq │ │ └── uniform.xml │ └── utest_py2jemris_script.py │ ├── rf_sim │ ├── animate_spins.py │ ├── rf_helpers.py │ ├── rf_sim_msi_single.py │ ├── rf_sim_spatial_spectral.py │ ├── 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