├── .gitignore ├── CHANGELOG.md ├── EPG_for_hmri_tbx ├── EPG-src │ ├── EPG_GRE.m │ ├── EPG_diffusion_weights.m │ ├── EPG_shift_matrices.m │ ├── E_diff.m │ └── RF_phase_cycle.m ├── Unit_Test_Protocol.json ├── lib │ └── d2r.m └── readme.txt ├── LICENSE ├── README.md ├── _config.yml ├── config ├── hmri_b1_standard_defaults.m ├── hmri_defaults.m ├── hmri_denoising_defaults.m ├── local │ ├── hmri_b1_local_defaults.m │ ├── hmri_local_defaults.m │ └── hmri_local_denoising_defaults.m └── readme.txt ├── docs ├── index.html ├── javascripts │ └── scale.fix.js ├── params.json └── stylesheets │ ├── github-light.css │ └── styles.css ├── etpm ├── Readme.txt ├── cp_update_TPM.m ├── eTPM.nii └── nwTPM_sl2.nii ├── examples ├── hmri_DIB_defaults.m ├── hmri_MTsat_Lipp2023_model_defaults.m ├── hmri_MTsat_Lipp_model_500deg_defaults.m ├── hmri_MTsat_Olsson2021_model_defaults.m ├── hmri_b1_local_defaults_bids.m ├── hmri_b1_local_defaults_example_1.m ├── hmri_local_defaults_errormaps.m └── hmri_local_defaults_example_1.m ├── hmri_autoreorient.m ├── hmri_calc_A.m ├── hmri_calc_MTsat.m ├── hmri_calc_R1.m ├── hmri_calc_R2s.m ├── hmri_calc_dMT.m ├── hmri_calc_dPD.m ├── hmri_calc_dR1.m ├── hmri_check_nifti_orientations.m ├── hmri_check_opt.m ├── hmri_code_tests ├── hmri_IO_test.m ├── hmri_MTsat_test.m ├── hmri_calc_A_test.m ├── hmri_calc_R1_test.m ├── hmri_calc_R2s_test.m ├── hmri_calc_errormaps_test.m ├── hmri_coreg_test.m ├── hmri_create_b1map_afi_test.m ├── hmri_function_template_test.m ├── hmri_get_ut_data.m ├── hmri_osf.m ├── hmri_proc_zero2nan_test.m ├── hmri_test_utils.m ├── hmri_webdav.m └── testconfig │ └── hmri_b1_local_defaults_test_afi_bids.m ├── hmri_coreg.m ├── hmri_corr_imperf_spoil.m ├── hmri_correct_MTsat.m ├── hmri_create_B1Map_process.m ├── hmri_create_B1Map_unwarp.m ├── hmri_create_FieldMap.m ├── hmri_create_MTProt.m ├── hmri_create_RFsens.m ├── hmri_create_b1map.m ├── hmri_create_comm_adjust.m ├── hmri_create_nifti.m ├── hmri_create_pm_brain_mask.m ├── hmri_create_pm_segment.m ├── hmri_create_unicort.m ├── hmri_denoising.m ├── hmri_get_defaults.m ├── hmri_get_version.m ├── hmri_log.m ├── hmri_proc_MPMsmooth.m ├── hmri_proc_crtMask.m ├── hmri_proc_zero2nan.m ├── hmri_quality_display.m ├── hmri_quiqi_build.m ├── hmri_quiqi_check.m ├── hmri_read_vols.m ├── hmri_run_create.m ├── hmri_run_create_B1.m ├── hmri_run_denoising.m ├── hmri_run_proc_US.m ├── hmri_run_proc_crtMask.m ├── hmri_run_proc_dartel_norm.m ├── hmri_run_proc_dartel_template.m ├── hmri_run_proc_dartel_warp.m ├── hmri_run_proc_pipeline.m ├── hmri_run_proc_smooth.m ├── hmri_wcomb_2mpms.m ├── install └── tbx_cfg_hmri_redirect.m ├── jar ├── Jama-mipav.jar ├── commons-math3-3.5.jar └── lcpca2.jar ├── mppca_denoise.m ├── spm12 ├── config │ ├── spm_cfg_dicom.m │ └── spm_run_dicom.m ├── metadata │ ├── anonymise_metadata.m │ ├── doc │ │ └── JSON_metadata_manual.pdf │ ├── find_field_name.m │ ├── get_jhdr_and_offset.m │ ├── get_metadata.m │ ├── get_metadata_val.m │ ├── 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