Skip to content

Commit

Permalink
Try explicit TOC
Browse files Browse the repository at this point in the history
  • Loading branch information
@mathieuboudreau
mathieuboudreau committed Oct 7, 2024
1 parent 72a7b4a commit 5aa72a0
Showing 1 changed file with 283 additions and 0 deletions.
283 changes: 283 additions & 0 deletions myst.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down

0 comments on commit 5aa72a0

Please sign in to comment.