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qmrlab

  • Key features
    • Data simulator
    • Data fitting and visualization
  • Methods available
    • UnderDevelopment
    • Processing
      • filter_map: Applies spatial filtering (2D or 3D)
    • QSM
      • qsm_sb: Fast quantitative susceptibility mapping
    • T1_relaxometry
      • vfa_t1: Compute a T1 map using Variable Flip Angle
      • mtv : Macromolecular Tissue Volume in brain
      • inversion_recovery: Compute a T1 map using Inversion Recovery data
      • mp2rage: Compute a T1 map using MP2RAGE
    • FieldMaps
      • b1_afi map: Actual Flip-Angle Imaging for B1+ mapping
      • b1_dam map: Double-Angle Method for B1+ mapping
      • b0_dem map : Dual Echo Method for B0 mapping
    • Noise
      • noise_level : Noise histogram fitting within a noise mask
      • denoising_mppca : 4d image denoising and noise map estimation
    • T2_relaxometry
      • mwf : Myelin Water Fraction from Multi-Exponential T2w data
      • mono_t2: Compute a monoexponential T2 map
    • Magnetization_transfer
      • qmt_bssfp : qMT using Balanced Steady State Free Precession acquisition
      • qmt_sirfse: qMT using Inversion Recovery Fast Spin Echo acquisition
      • mt_sat : Correction of Magnetization transfer for RF inhomogeneities and T1
      • qmt_spgr: quantitative Magnetizatoion Transfer (qMT) using Spoiled Gradient Echo
      • mt_ratio : Magnetization transfer ratio (MTR)
    • Diffusion
      • dti: Compute a tensor from diffusion data
      • noddi: Neurite Orientation Dispersion and Density Imaging
      • charmed: Composite Hindered and Restricted Model for Diffusion
  • Protocols
    • mp2rage
      • NumberOfShots
      • Repetition Times
      • Inversion Times
      • Flip Angles

Installation

  • How to install
    • qMRLab in MATLAB
    • qMRLab in Octave
    • qMRLab in Docker šŸ³
    • How to cite?
  • Known issues
    • OSX
    • Apple Silicon (M1) compatibility

Getting Started

  • Beginnerā€™s example with GUI
    • 1. Open matlab
    • 2. Run startup
    • 3. Launch the GUI
    • 4. Model selection
    • 5. Download example data
    • 6. View the data
    • 7. Set up the protocol
    • 8. View the data fit in 1 voxel
    • 9. Fit the whole dataset
  • Beginnerā€™s example with CLI
    • 1. Open MATLAB and setup path
    • 2. Generate a batch example
    • 3. Run the batch
  • Example datasets
    • Download example datasets via GUI
    • Download example datasets via CLI

User Interface Guidelines

  • Interfaces
    • Graphical User Interface (GUI)
      • 1. Startup
      • 2. Layout
        • 2.1 Menu Panel
        • 2.2 Main Panel
        • 2.3 Options Panel
      • 3. Data Viewer
      • 4. Data Fitting
        • 4.1 Data format
        • 4.2 Fitting Procedure
        • 4.3 Viewing the fit results
      • 5. Simulation
        • 5.1. Single Voxel Curve
        • 5.2. Sensitivity Analysis
        • 5.3. Multi Voxel Distribution
      • 6. Options Panel
        • 6.1 Protocol
        • 6.2. Fitting
        • 6.3. Options
      • 7. Tutorial
    • Command Line Interface (CLI)
      • General structure
      • General commands
      • Model structure
        • All models have the following properties:
        • And functions:
        • Most models have these additional functions:

Workflows

  • qMRFlow
    • About
    • Benefits
    • Use qMRFlow with Docker šŸ³
    • Use qMRFlow locally
  • Available pipelines
    • MagnetizationTransfer
      • MTsat: Magnetization transfer saturation
        • Usage
        • Description
        • Container requirements
        • Local installation requirements
        • Folder organization
        • Optional arguments
        • Notes
        • Reference
      • MTR: Magnetization transfer ratio
        • Usage
        • Description
        • Container requirements
        • Local installation requirements
        • Folder organization
        • Optional arguments
        • Notes
        • Reference

Open Pulse Sequences

  • qMRPullseq
    • About
    • VFA T1 mapping

Contribute

  • Developerā€™s Documentation
qMRLab
  • Docs »
  • Interfaces
  • Edit on GitHub

InterfacesĀ¶

  • Graphical User Interface (GUI)
    • 1. Startup
    • 2. Layout
    • 3. Data Viewer
    • 4. Data Fitting
    • 5. Simulation
    • 6. Options Panel
    • 7. Tutorial
  • Command Line Interface (CLI)
    • General structure
    • General commands
    • Model structure
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