Contents

• Contents
• Introduction
  • The intrinsic MR signal
  • Excitation and relaxation
  • Image formation
• Signal and noise in MRI
  • Introduction
  • The MR signal
    • Imaging parameters
  • The noise
    • Thermal noise
    • Sample losses
    • Imaging parameters
    • Structured noise
• Probability density functions of MR data
  • Introduction
  • PDF of raw MR data
  • PDF of magnitude data
    • The Rice distribution
    • The generalized Rice distribution
  • PDF of phase data
• Noise estimation
  • Introduction
  • Parameter estimation
    • Minimum Variance Bound
    • Maximum Likelihood estimation
  • Noise estimation
    • Single image methods
    • Double image method
  • Experiments and discussion
  • Conclusions
• Signal estimation
  • Introduction
  • Signal estimation from Rice distributed data
    • Conventional approach
    • Maximum Likelihood estimation
    • Experiments and discussion
  • Signal estimation from PCMR data
    • Methods
    • Experiments and discussion
  • Combined signal and noise estimation
  • Conclusions
• Application: T₁ and T₂ estimation
  • Introduction
  • Method
    • Magnitude data PDF
    • Errors introduced in T₁ and T₂ estimation
    • Maximum Likelihood estimation
  • Experiments and Discussion
    • Simulation experiments
    • T₁-map estimation
    • T₂-map estimation
  • Conclusions
• SNR estimation
  • Introduction
    • Single image methods
    • The NEMA standard
  • Cross correlation method
    • Theory
    • Experiment
  • Results and discussion
• SNR Improvement
  • Introduction
  • Time averaging
  • Spatial averaging
    • Cross correlation
    • Anisotropic adaptive diffusion filter
  • Conclusions
• 3D Image Segmentation
  • Introduction
  • 3D semi-interactive segmentation
    • Immersion-based watershed algorithm
    • Reduction of oversegmentation
    • Interactive segmentation
  • Experiments and discussion
    • Materials
    • Phantom object data
    • Mouse data
  • Applications
    • Fragile X knockout mice
    • Canary brain
  • Conclusions
• Conclusions
• Bibliography
• The generalized Rice PDF
  • PDF of one PCMR pixel variable
  • PDF of the average of squared PCMR pixel variables
• List of symbols and abbreviations
  • Greek symbols
  • Roman symbols
  • Abbreviations
• Nederlandse samenvatting
• Personalia
  • Curriculum Vitae
  • List of publications
    • Journal papers
    • Conference Proceedings