Contents

• Introduction
  • The Design of Monalisa
  • A few Definitions
  • A Quick View at the List of our Reconstructions
• Reconstruction Calls
  • Input Arguments for Reconstruction Functions
  • Non-Cartesian Static Reconstructions
    • Mathilda, the Initial Image-Reconstruction
    • Sensa
    • Steva
    • Sleva
  • Deformation-Fields
  • Non-Cartesian Chain Reconstructions
    • TevaMorphosia_chain
    • TevaDuoMorphosia_chain
    • SensitivaMorphosia_chain
    • SensitivaDuoMorphosia_chain
  • Non-Cartesian Sheet Reconstructions
    • TevaMorphosia_sheet
    • SensitivaMorphosia_sheet
  • Partial-Cartesian Static Reconstructions
  • Partial-Cartesian Chain Reconstructions
• The Mitosius
  • Prerequisites
  • Usage instructions
    • Define the Paths
    • Load the Raw Data
    • Add MRI Acquisition Parameters
    • Read the raw data and compute trajectory points, volume elements
    • Load the Coil Sensitivity Matrix
    • Normalize the data
    • Cleaning of the mask
    • Compute Final Data Structures for Reconstruction
    • Save the Results
  • Notes
• Binning: Flexible Readout Rearrangement
  • First Example: Sequential Binning
    • Steps for Sequential Binning
  • Second Example: Task-Based (Hi-Fi) fMRI
    • Steps for Hi-Fi Binning:
  • Third Example: Respiratory Binning for Motion-Resolved Cardiac MRI using Superior-Inferior (SI) Projections
    • Steps for Respiratory Binning using SI projections:
  • Fourth Example: Cardiac Binning for Motion-Resolved Cardiac MRI using Superior-Inferior (SI) Projections
    • Steps for Cardiac Binning using SI projections:
• Coil Sensitivity Map Estimation
  • Coil sensitivity from pre-scan images
  • Coil sensitivity from raw data pre-scans
  • Automated Estimation
  • Manual Estimation
    • Acquisition Parameters
    • Mask Creation
    • Sensitivity Approximation
  • Code Explanation
    • Path selection
    • Parameters
    • Data extraction
    • Gridding Matrices
    • Mask Creation
    • Coil Sensitivity Estimation
    • Improved Estimation
• Acquisition Guidelines for Coil Sensitivity Estimation using Prescans
• Volume Elements or Density Compensation
  • What are Volume Elements? Basic Usage
  • Ok, but why are there Volume Elements?
• Trajectory Definition in Monalisa
  • What is a Trajectory? Basic Usage
  • Custom Trajectories
• Reading Raw Data
  • Basic Usage
  • Advanced Details for Developers

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