diff --git a/myst.yml b/myst.yml index cea4cf4..b9ceea2 100644 --- a/myst.yml +++ b/myst.yml @@ -60,6 +60,289 @@ project: - bibliography/ir.bib resources: - figures/2 T1 mapping/figure2-2.ipynb + toc: + # Auto-generated by `myst init --write-toc` + - file: index.md + - file: README.md + - title: Introduction To QMRI + children: + - file: 1 Introduction to qMRI/01-intro.md + - file: 1 Introduction to qMRI/02-million_dollar.md + - file: 1 Introduction to qMRI/03-journey.md + - file: 1 Introduction to qMRI/04-encode.md + - file: 1 Introduction to qMRI/05-sequences.md + - file: 1 Introduction to qMRI/06-qmri_practice.md + - title: T1 Mapping + children: + - title: Inversion Recovery + children: + - file: 2 T1 Mapping/2-1 Inversion Recovery/01-introduction.md + - file: 2 T1 Mapping/2-1 Inversion Recovery/02-IR_SignalModelling.md + - file: 2 T1 Mapping/2-1 Inversion Recovery/03-IR_DataFitting.md + - file: 2 T1 Mapping/2-1 Inversion Recovery/04-IR_BenefitsAndPitfalls.md + - file: 2 T1 Mapping/2-1 Inversion Recovery/05-IR_OtherMethods.md + - title: Variable Flip Angle + children: + - file: 2 T1 Mapping/2-2 Variable Flip Angle/01-Introduction.md + - file: 2 T1 Mapping/2-2 Variable Flip Angle/02-VFA_SignalModelling.md + - file: 2 T1 Mapping/2-2 Variable Flip Angle/03-VFA_DataFitting.md + - file: 2 T1 Mapping/2-2 Variable Flip Angle/04-VFA_BenefitsAndPitfalls.md + - title: MP2RAGE + children: + - file: 2 T1 Mapping/2-3 MP2RAGE/01-Introduction.md + - file: 2 T1 Mapping/2-3 MP2RAGE/02-SignalModelling.md + - file: 2 T1 Mapping/2-3 MP2RAGE/03-DataFitting.md + - file: 2 T1 Mapping/2-3 MP2RAGE/04-BenefitsAndPitfalls.md + - title: Exercises + children: + - file: 2 T1 Mapping/2-4 Exercises/01-Exercises.md + - title: T2 Mapping + children: + - title: Introduction + children: + - file: 3 T2 Mapping/01-Introduction/01-Introduction.md + - file: 3 T2 Mapping/01-Introduction/02-T2 mapping vs T2-weighted imaging.md + - title: Monoexponential T2 Mapping + children: + - file: 3 T2 Mapping/02-Monoexponential T2 Mapping/01-Introduction.md + - file: 3 T2 Mapping/02-Monoexponential T2 Mapping/02-Signal modelling.md + - title: Data Fitting + children: + - file: >- + 3 T2 Mapping/02-Monoexponential T2 Mapping/03-Data + Fitting/00-Foreward.md + - file: >- + 3 T2 Mapping/02-Monoexponential T2 Mapping/03-Data + Fitting/01-T2*.md + - file: >- + 3 T2 Mapping/02-Monoexponential T2 Mapping/03-Data + Fitting/02-Noise.md + - file: >- + 3 T2 Mapping/02-Monoexponential T2 Mapping/04-Benefits and + pitfalls.md + - title: Multiexponential T2 Mapping + children: + - file: 3 T2 Mapping/03-Multiexponential T2 Mapping/01-Introduction.md + - file: 3 T2 Mapping/03-Multiexponential T2 Mapping/02-SignalModelling.md + - file: 3 T2 Mapping/03-Multiexponential T2 Mapping/03-DataFitting.md + - title: Applications + children: + - file: >- + 3 T2 Mapping/03-Multiexponential T2 + Mapping/04-Applications/01-Myelin water fraction (MWF) + imaging.md + - file: >- + 3 T2 Mapping/03-Multiexponential T2 + Mapping/04-Applications/02-T2* and quantitative susceptibility + mapping (QSM).md + - file: >- + 3 T2 Mapping/03-Multiexponential T2 + Mapping/04-Applications/03-Benefits and pitfalls of + multi-exponential T2 mapping.md + - title: B1 Mapping + children: + - title: Double Angle Methods + children: + - file: >- + 4 B1 Mapping/01-Double Angle technique/01-Transmit and Receive RF + field amplitudes.md + - file: 4 B1 Mapping/01-Double Angle technique/02-Double Angle method(s).md + - file: >- + 4 B1 Mapping/01-Double Angle technique/03- Gradient echo and 180 deg + spin echo method copy.md + - file: 4 B1 Mapping/01-Double Angle technique/A1-Appendix A.md + - title: Actual Flip Angle Imaging + children: + - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/01-abstract.md + - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/02-SignalModeling.md + - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/03-DataFitting.md + - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/04-BenefitsAndPitfalls.md + - title: Filtering + children: + - file: 4 B1 Mapping/03-Filtering/01-Introduction.md + - file: 4 B1 Mapping/03-Filtering/02-Filters and smoothing.md + - file: 4 B1 Mapping/03-Filtering/03-1D examples.md + - file: 4 B1 Mapping/03-Filtering/04-B1 map examples.md + - file: >- + 4 B1 Mapping/03-Filtering/05-Recommendations, benefits, and + pitfalls.md + - title: B0 Mapping + children: + - title: B0 Inhomogeneities + children: + - file: 5 B0 Mapping/1 B0 Inhomogeneities/1-Introduction.md + - title: Sources + children: + - file: 5 B0 Mapping/1 B0 Inhomogeneities/2-Sources/01-Hardware.md + - file: >- + 5 B0 Mapping/1 B0 Inhomogeneities/2-Sources/02-Magnetic + susceptibility.md + - file: 5 B0 Mapping/1 B0 Inhomogeneities/3-Effects on signal.md + - title: Dual Echo B0 Mapping + children: + - file: 5 B0 Mapping/2 Dual echo B0 mapping/01-Introduction.md + - file: 5 B0 Mapping/2 Dual echo B0 mapping/02-Signal Theory.md + - file: >- + 5 B0 Mapping/2 Dual echo B0 mapping/03-Single Frequency + Population.md + - file: 5 B0 Mapping/2 Dual echo B0 mapping/04-Multi-Frequency Population.md + - file: 5 B0 Mapping/2 Dual echo B0 mapping/05-Benefits and Pitfalls.md + - title: Phase Unwrapping + children: + - file: 5 B0 Mapping/3 Phase Unwrapping/01-Introduction.md + - file: 5 B0 Mapping/3 Phase Unwrapping/02-Temporal Unwrapping.md + - file: 5 B0 Mapping/3 Phase Unwrapping/03-Spatial Unwrapping.md + - file: 5 B0 Mapping/3 Phase Unwrapping/04-Phase unwrapping ambiguity.md + - file: >- + 5 B0 Mapping/3 Phase Unwrapping/05-Problematic phase map + properties.md + - file: 5 B0 Mapping/3 Phase Unwrapping/06-Software.md + - title: Advanced B0 Mapping Methods + children: + - file: 5 B0 Mapping/4 Advanced B0 Mapping Methods/01-Introduction.md + - file: 5 B0 Mapping/4 Advanced B0 Mapping Methods/02-MultiEcho.md + - file: >- + 5 B0 Mapping/4 Advanced B0 Mapping Methods/03-Reducing eddy + currents.md + - file: 5 B0 Mapping/4 Advanced B0 Mapping Methods/04-Realtime.md + - file: 5 B0 Mapping/5 Conclusion/5 Conclusion.md + - title: Magnetization Transfer Imaging + children: + - title: Quantitative Magnetization Transfer + children: + - file: >- + 6 Magnetization Transfer Imaging/1 Quantitative Magnetization + Transfer/01-abstract.md + - file: >- + 6 Magnetization Transfer Imaging/1 Quantitative Magnetization + Transfer/02-SignalModelling.md + - file: >- + 6 Magnetization Transfer Imaging/1 Quantitative Magnetization + Transfer/03-DataFitting.md + - file: >- + 6 Magnetization Transfer Imaging/1 Quantitative Magnetization + Transfer/04-Summary.md + - title: Magnetization Transfer Ratio + children: + - file: >- + 6 Magnetization Transfer Imaging/2 Magnetization Transfer + Ratio/01-Introduction.md + - file: >- + 6 Magnetization Transfer Imaging/2 Magnetization Transfer + Ratio/02-MTR in theory.md + - file: >- + 6 Magnetization Transfer Imaging/2 Magnetization Transfer + Ratio/03-MTR in practice.md + - file: >- + 6 Magnetization Transfer Imaging/2 Magnetization Transfer + Ratio/04-Parting Thoughts.md + - file: >- + 6 Magnetization Transfer Imaging/2 Magnetization Transfer Ratio/A1- + Appendix A.md + - title: Magnetization Transfer Saturation + children: + - file: >- + 6 Magnetization Transfer Imaging/3 Magnetization Transfer + Saturation/01-Introduction.md + - file: >- + 6 Magnetization Transfer Imaging/3 Magnetization Transfer + Saturation/02-Theory.md + - file: >- + 6 Magnetization Transfer Imaging/3 Magnetization Transfer + Saturation/03-Simulations.md + - file: >- + 6 Magnetization Transfer Imaging/3 Magnetization Transfer + Saturation/A1-Appendix A.md + - file: >- + 6 Magnetization Transfer Imaging/3 Magnetization Transfer + Saturation/A2-Appendix B.md + - title: Figures + children: + - title: T1 Mapping + children: + - file: Figures/2 T1 mapping/figure_2-2.ipynb + - file: Figures/2 T1 mapping/figure_2-3.ipynb + - file: Figures/2 T1 mapping/figure_2-4.ipynb + - file: Figures/2 T1 mapping/figure_2-5.ipynb + - file: Figures/2 T1 mapping/figure_2-6.ipynb + - file: Figures/2 T1 mapping/figure_vfa2.ipynb + - file: Figures/2 T1 mapping/figure_vfa3.ipynb + - file: Figures/2 T1 mapping/figure_vfa4.ipynb + - file: Figures/2 T1 mapping/figure_vfa5.ipynb + - file: Figures/2 T1 mapping/figure_vfa6.ipynb + - file: Figures/2 T1 mapping/figure_vfa7.ipynb + - file: Figures/2 T1 mapping/foreword.md + - file: Figures/2 T1 mapping/mp2rageFig1.ipynb + - file: Figures/2 T1 mapping/mp2rageFig2.ipynb + - title: T2 Mapping + children: + - file: Figures/3 T2 mapping/fig3p1.ipynb + - file: Figures/3 T2 mapping/fig3p2.ipynb + - file: Figures/3 T2 mapping/fig3p3.ipynb + - file: Figures/3 T2 mapping/fig3p4.ipynb + - file: Figures/3 T2 mapping/fig3p5.ipynb + - title: B1 Mapping + children: + - file: Figures/4 B1 mapping/afiFig1.ipynb + - file: Figures/4 B1 mapping/afiFig2.ipynb + - file: Figures/4 B1 mapping/afiFig3.ipynb + - file: Figures/4 B1 mapping/afiFig4.ipynb + - file: Figures/4 B1 mapping/afiFig5.ipynb + - file: Figures/4 B1 mapping/afiFig6.ipynb + - file: Figures/4 B1 mapping/afiFig7.ipynb + - file: Figures/4 B1 mapping/afiFig8.ipynb + - file: Figures/4 B1 mapping/daFig1.ipynb + - file: Figures/4 B1 mapping/daFig2.ipynb + - file: Figures/4 B1 mapping/daFig3.ipynb + - file: Figures/4 B1 mapping/filtFig1.ipynb + - file: Figures/4 B1 mapping/filtFig2.ipynb + - file: Figures/4 B1 mapping/filtFig3.ipynb + - file: Figures/4 B1 mapping/filtFig4.ipynb + - file: Figures/4 B1 mapping/filtFig5.ipynb + - file: Figures/4 B1 mapping/filtFig6.ipynb + - file: Figures/4 B1 mapping/filtFig7.ipynb + - file: Figures/4 B1 mapping/filtFig8.ipynb + - file: Figures/4 B1 mapping/filtFig9.ipynb + - title: B0 Mapping + children: + - file: Figures/5 B0 mapping/fig5p1.ipynb + - file: Figures/5 B0 mapping/fig5p2.ipynb + - file: Figures/5 B0 mapping/fig5p3.ipynb + - file: Figures/5 B0 mapping/fig5p4.ipynb + - file: Figures/5 B0 mapping/fig5p5.ipynb + - file: Figures/5 B0 mapping/fig5p6.ipynb + - file: Figures/5 B0 mapping/fig5p7.ipynb + - file: Figures/5 B0 mapping/fig5p8.ipynb + - file: Figures/5 B0 mapping/fig5p9.ipynb + - file: Figures/5 B0 mapping/fig5p10.ipynb + - file: Figures/5 B0 mapping/fig5p11.ipynb + - file: Figures/5 B0 mapping/fig5p12.ipynb + - file: Figures/5 B0 mapping/fig5p13.ipynb + - file: Figures/5 B0 mapping/fig5p14.ipynb + - file: Figures/5 B0 mapping/fig5p15.ipynb + - file: Figures/5 B0 mapping/fig5p16.ipynb + - file: Figures/5 B0 mapping/fig5p17.ipynb + - file: Figures/5 B0 mapping/fig5p18.ipynb + - title: MT + children: + - file: Figures/6 MT/mtrFig1.ipynb + - file: Figures/6 MT/mtrFig2.ipynb + - file: Figures/6 MT/mtrFig3.ipynb + - file: Figures/6 MT/mtrFig4.ipynb + - file: Figures/6 MT/mtrFig5.ipynb + - file: Figures/6 MT/mtsatAppendixB1.ipynb + - file: Figures/6 MT/mtsatAppendixB2.ipynb + - file: Figures/6 MT/mtsatAppendixB3.ipynb + - file: Figures/6 MT/mtsatFig1.ipynb + - file: Figures/6 MT/mtsatFig2.ipynb + - file: Figures/6 MT/mtsatFig3.ipynb + - file: Figures/6 MT/qmtFig1.ipynb + - file: Figures/6 MT/qmtFig2.ipynb + - file: Figures/6 MT/qmtFig3.ipynb + - file: Figures/6 MT/qmtFig4.ipynb + - file: Figures/6 MT/qmtFig5.ipynb + - file: Figures/6 MT/qmtFig6.ipynb + site: template: book-theme options: