myst.yml

# See docs at: https://mystmd.org/guide/frontmatter
version: 1
project:
  title: 'Quantitative MRI mOOC'
  subtitle: An interactive book on the fundamentals of qMRI
  copyright: NeuroPoly 2024
  thumbnail: public/icon.png
  thebe:
    binder:
      url: https://mybinder.org
      repo: qmrlab/mooc
      ref: mb/dev
  keywords:
    - quantitative MRI
    - education
  github: https://github.com/qmrlab/mooc
  banner: banner.jpg
  venue: qMRLab
  subject: mOOC
  numbering:
    headings: true
  open_access: true
  license: CC-BY-4.0
  date: 2024-10-08
  exports:
    - format: pdf
  abbreviations:
    MRI: Magnetic resonance imaging
    MR: Magnetic resonance
    NMR: Nuclear Magnetic Resonance
    qMRI: quantitative magnetic resonance imaging
    GPT: Generative Pre-trained Transformer
    MRM: Magnetic Resonance in Medicine
    B0: Main magnetic field
    B1: Radiofrequency field
    FID: Free Induction Decay
    Gx: X-axis gradient  
    Gy: Y-axis gradient
    Gz: Z-axis gradient
    TR: Repetition Time
    TE: Echo Time
    TI: Inversion Time
    CSF: Cerebrospinal fluid
    T1: Longitudinal magnetization relaxation time constant
    _T_{sub}`1`: Longitudinal magnetization relaxation time constant
    T2: Transverse magnetization relaxation time constant
    SE: Spin Echo
    GRE: Gradient Echo
    SPGR: Spoiled Gradient Echo (sequence)
    UMAP: Uniform manifold approximation and projection
    ADC: Analog to digital converter
    RF: Radiofrequency
    FA: Flip Angle
    VFA: Variable Flip Angle
    DESPOT1: Driven Equilibrium Single Pulse Observation of _T_{sub}`1`
    SNR: Signal-to-noise ratio
    RD-NLS: reduced-dimension non-linear least-squares
    STD: Standard deviation
    MT: Magnetization Transfer
    MTR: Magnetization Transfer Ratio
    MS: Multiple Sclerosis
    qMT: Quantitative Magnetization Transfer
    MTsat: Magnetization Transfer saturation
    SAR: Specific absorption rate
  exclude:
    - README.md
    - LICENSE.md
    - venv/*
  bibliography:
    - bibliography/book.bib
    - bibliography/ir.bib
    - bibliography/b0chapter.bib
    - bibliography/t2chapter.bib
    - bibliography/t1chapter.bib
    - bibliography/doubleangle.bib
    - bibliography/afi.bib
    - bibliography/filtering.bib
    - bibliography/qmtchapter.bib
    - bibliography/mtrchapter.bib
    - bibliography/mtsatchapter.bib
  resources:
    - figures/2 T1 mapping/figure2-2.ipynb
  toc:
    # Auto-generated by `myst init --write-toc` and then edited by MB
    - file: index.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: Notebooks
              children:
                - file: 2 T1 Mapping/2-1 Inversion Recovery/Notebooks/Figure-2-1-1.ipynb
                - file: 2 T1 Mapping/2-1 Inversion Recovery/Notebooks/Figure-2-1-2.ipynb
                - file: 2 T1 Mapping/2-1 Inversion Recovery/Notebooks/Figure-2-1-3.ipynb
                - file: 2 T1 Mapping/2-1 Inversion Recovery/Notebooks/Figure-2-1-4.ipynb
                - file: 2 T1 Mapping/2-1 Inversion Recovery/Notebooks/Figure-2-1-5.ipynb
        - 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: Notebooks
              children:
                - file: 2 T1 Mapping/2-2 Variable Flip Angle/Notebooks/Figure-2-2-1.ipynb
                - file: 2 T1 Mapping/2-2 Variable Flip Angle/Notebooks/Figure-2-2-2.ipynb
                - file: 2 T1 Mapping/2-2 Variable Flip Angle/Notebooks/Figure-2-2-3.ipynb
                - file: 2 T1 Mapping/2-2 Variable Flip Angle/Notebooks/Figure-2-2-4.ipynb
                - file: 2 T1 Mapping/2-2 Variable Flip Angle/Notebooks/Figure-2-2-5.ipynb
                - file: 2 T1 Mapping/2-2 Variable Flip Angle/Notebooks/Figure-2-2-6.ipynb
        - 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: Notebooks
              children:
                - file: 2 T1 Mapping/2-3 MP2RAGE/Notebooks/Figure-2-3-1.ipynb
                - file: 2 T1 Mapping/2-3 MP2RAGE/Notebooks/Figure-2-3-2.ipynb
        - file: 2 T1 Mapping/2-4 Exercises/01-Exercises.md
    - title: T2 Mapping
      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: Notebooks
              children:
                - file: 3 T2 Mapping/02-Monoexponential T2 Mapping/Notebooks/Figure-3-2-1.ipynb
                - file: 3 T2 Mapping/02-Monoexponential T2 Mapping/Notebooks/Figure-3-2-2.ipynb
        - 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: Notebooks
              children:
              - file: 3 T2 Mapping/03-Multiexponential T2 Mapping/Notebooks/Figure-3-3-1.ipynb
            - title: Notebooks
              children:
              - file: 3 T2 Mapping/03-Multiexponential T2 Mapping/Notebooks/Figure-3-3-2.ipynb
        - title: Notebooks
          children:
            - file: 3 T2 Mapping/01-Introduction/Notebooks/Figure-3-1-1.ipynb
    - 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.md
            - file: 4 B1 Mapping/01-Double Angle technique/A1-Appendix A.md
            - title: Notebooks
              children:
                - file: 4 B1 Mapping/01-Double Angle technique/Notebooks/Figure-4-1-1.ipynb
                - file: 4 B1 Mapping/01-Double Angle technique/Notebooks/Figure-4-1-2.ipynb
                - file: 4 B1 Mapping/01-Double Angle technique/Notebooks/Figure-4-1-3.ipynb
        - 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: Notebooks
              children:
                - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/Notebooks/Figure-4-2-1.ipynb
                - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/Notebooks/Figure-4-2-2.ipynb
                - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/Notebooks/Figure-4-2-3.ipynb
                - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/Notebooks/Figure-4-2-4.ipynb
                - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/Notebooks/Figure-4-2-5.ipynb
                - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/Notebooks/Figure-4-2-6.ipynb
                - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/Notebooks/Figure-4-2-7.ipynb
                - file: 4 B1 Mapping/02-Actual Flip Angle Imaging/Notebooks/Figure-4-2-8.ipynb
        - 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: Notebooks
              children:
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-1.ipynb
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-2.ipynb
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-3.ipynb
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-4.ipynb
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-5.ipynb
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-6.ipynb
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-7.ipynb
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-8.ipynb
                - file: 4 B1 Mapping/03-Filtering/Notebooks/Figure-4-3-9.ipynb
    - 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: Notebooks
              children:
                - file: 5 B0 Mapping/1 B0 Inhomogeneities/Notebooks/Figure-5-1-1.ipynb
                - file: 5 B0 Mapping/1 B0 Inhomogeneities/Notebooks/Figure-5-1-2.ipynb
                - file: 5 B0 Mapping/1 B0 Inhomogeneities/Notebooks/Figure-5-1-3.ipynb
                - file: 5 B0 Mapping/1 B0 Inhomogeneities/Notebooks/Figure-5-1-4.ipynb
                - file: 5 B0 Mapping/1 B0 Inhomogeneities/Notebooks/Figure-5-1-5.ipynb
        - 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: Notebooks
              children:
                - file: 5 B0 Mapping/2 Dual echo B0 mapping/Notebooks/Figure-5-2-1.ipynb
                - file: 5 B0 Mapping/2 Dual echo B0 mapping/Notebooks/Figure-5-2-2.ipynb
                - file: 5 B0 Mapping/2 Dual echo B0 mapping/Notebooks/Figure-5-2-3.ipynb
                - file: 5 B0 Mapping/2 Dual echo B0 mapping/Notebooks/Figure-5-2-4.ipynb
        - 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: Notebooks
              children:
                - file: 5 B0 Mapping/3 Phase Unwrapping/Notebooks/Figure-5-3-1.ipynb
                - file: 5 B0 Mapping/3 Phase Unwrapping/Notebooks/Figure-5-3-2.ipynb
                - file: 5 B0 Mapping/3 Phase Unwrapping/Notebooks/Figure-5-3-3.ipynb
                - file: 5 B0 Mapping/3 Phase Unwrapping/Notebooks/Figure-5-3-4.ipynb
                - file: 5 B0 Mapping/3 Phase Unwrapping/Notebooks/Figure-5-3-5.ipynb
        - 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
            - title: Notebooks
              children:
                - file: 5 B0 Mapping/4 Advanced B0 Mapping Methods/Notebooks/Figure-5-4-1.ipynb
                - file: 5 B0 Mapping/4 Advanced B0 Mapping Methods/Notebooks/Figure-5-4-2.ipynb
                - file: 5 B0 Mapping/4 Advanced B0 Mapping Methods/Notebooks/Figure-5-4-3.ipynb
                - file: 5 B0 Mapping/4 Advanced B0 Mapping Methods/Notebooks/Figure-5-4-4.ipynb
        - 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: Notebooks
              children:
                - file: >-
                    6 Magnetization Transfer Imaging/1 Quantitative Magnetization
                    Transfer/Notebooks/Figure-6-1-1.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/1 Quantitative Magnetization
                    Transfer/Notebooks/Figure-6-1-2.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/1 Quantitative Magnetization
                    Transfer/Notebooks/Figure-6-1-3.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/1 Quantitative Magnetization
                    Transfer/Notebooks/Figure-6-1-4.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/1 Quantitative Magnetization
                    Transfer/Notebooks/Figure-6-1-5.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/1 Quantitative Magnetization
                    Transfer/Notebooks/Figure-6-1-6.ipynb
        - 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: Notebooks
              children:
                - file: >-
                    6 Magnetization Transfer Imaging/2 Magnetization Transfer
                    Ratio/Notebooks/Figure-6-2-1.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/2 Magnetization Transfer
                    Ratio/Notebooks/Figure-6-2-2.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/2 Magnetization Transfer
                    Ratio/Notebooks/Figure-6-2-3.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/2 Magnetization Transfer
                    Ratio/Notebooks/Figure-6-2-4.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/2 Magnetization Transfer
                    Ratio/Notebooks/Figure-6-2-5.ipynb

        - 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: Notebooks
              children:
                - file: >-
                    6 Magnetization Transfer Imaging/3 Magnetization Transfer
                    Saturation/Notebooks/Figure-6-3-1.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/3 Magnetization Transfer
                    Saturation/Notebooks/Figure-6-3-2.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/3 Magnetization Transfer
                    Saturation/Notebooks/Figure-6-3-3.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/3 Magnetization Transfer
                    Saturation/Notebooks/Figure-6-3-B1.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/3 Magnetization Transfer
                    Saturation/Notebooks/Figure-6-3-B2.ipynb
                - file: >-
                    6 Magnetization Transfer Imaging/3 Magnetization Transfer
                    Saturation/Notebooks/Figure-6-3-B3.ipynb
site:
  template: book-theme
  options:
    logo: public/icon.png
    logo_text: qMRI mOOC
  actions:
    - title: Discussions
      url: https://github.com/qMRLab/mooc/discussions
    - title: qMRLab
      url: https://qmrlab.org
    - title: NeuroPoly
      url: https://neuro.polymtl.ca/