QMRITools demonstration

The release contains a zip file DemoAndTest.zip in which there is a file demo.nb and a folder DemoData. To have a global overview of the functionality of the toolbox you can download this folder and run the demo.nb. By default the demo.nb looks for the folders DemoData in the same folder as the notebook.

The demo.nb contains the following demonstrations.

Initialization up

  • Loading the toolbox definitions
  • Verbose loading
  • List all Packages and toolboxes
  • Memory Usage

Basic Data manipulation and visualisation up

  • Importing Data
  • Plotting data Data
  • Automatically find cross section images
  • Rescaling Data
  • Cropping
    • Automatic crop
    • Apply To Rescaled Data
    • Manual crop
    • Reverse the Crop
  • Splitting Data - Split and Stitch - Example make both legs left
  • Joining multiple stacks

General functions up

  • Define Data
  • Data Operations
  • Filters
  • Operation ignoring zeros

Masking up

  • Import Data
  • Create Mask
    • Automated and threshold masking
    • Manual segmentation processing
    • Splitting segmentation in slice direction
    • Extract Data from Masks
  • Rescaling Segmentations

Registration using Elastix up

  • Import Data
  • Affine Transformation
  • B-spline Registration of two legs
    • Full Registration
    • Constrained in one direction
  • Register And Apply to other Data

Dixon and Phase unwrapping up

  • Simulated phase unwrapping
    • Simulate some Data
    • Unwrap simulated Data
  • Dixon data
    • Import Data
    • Create a B0Map from phase data
    • Calculate a T2 star map from the echos
    • Perform iDeal reconstruction with initial B0 and T2star

Simulate Dixon Data and fit testing up

  • Simulate the Dixon signal
  • Fit the simulated Dixon signal
  • Evaluate the fits

ME-SE (TSE) T2 mapping up

  • Import Data
  • Define Slice Profiles
  • calibrate and Fit the data

Simulate EPG Data and fit testing up

  • Simulate the EPG signal
  • Fit the simulated EPG signal
  • Evaluate the fits

DTI and IVIM up

  • Generating diffusion gradients
  • Import The Data
  • Prep the IVIM and DTI data
    • Sort and mask
    • Denoise DWI data
    • Motion and eddy current correction
  • IVIM Fitting
    • Whole volume calibrate
    • IVIM fit
    • Split signals into perfusion and diffusion
  • Tensor analysis
    • Fit the tensors
    • Analyse Tensor parameters
    • Calculate Tensor angles

Simulate Tensor Data and fit testing up

  • Simulate Diffusion signal
  • Fit the simulated diffusion signal
  • Evaluate the fits

Fiber Tractography up

  • Import The Data
  • Process the data for tractography
  • Fiber Tractography

J-coupling simulations up

  • Spin systems
    • Predefined spin systems
    • Custom spin systems
  • Glutamate spectra with Steam
  • Simulate Fat Spectra
    • PulseAcquire
    • Spin echo
    • STEAM
  • Fat STEAM with various TEs

Cardiac data processing and simulation up

  • Simulate Cardiac Shape
  • Analyse Cardiac shape
  • Cardiac Segmentation
    • perform segmentation
    • Analyse data based on segmentation
    • Visualize results