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 
- Loading the toolbox definitions
- Verbose loading
- List all Packages and toolboxes
- Memory Usage
Basic Data manipulation and visualisation 
- 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 
- Define Data
- Data Operations
- Filters
- Operation ignoring zeros
Masking 
- 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 
- 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 
- 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 
- Simulate the Dixon signal
- Fit the simulated Dixon signal
- Evaluate the fits
ME-SE (TSE) T2 mapping 
- Import Data
- Define Slice Profiles
- calibrate and Fit the data
Simulate EPG Data and fit testing 
- Simulate the EPG signal
- Fit the simulated EPG signal
- Evaluate the fits
DTI and IVIM 
- 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 
- Simulate Diffusion signal
- Fit the simulated diffusion signal
- Evaluate the fits
Fiber Tractography 
- Import The Data
- Process the data for tractography
- Fiber Tractography
J-coupling simulations 
- 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 
- Simulate Cardiac Shape
- Analyse Cardiac shape
- Cardiac Segmentation
- perform segmentation
- Analyse data based on segmentation
- Visualize results