mwf : Myelin Water Fraction from Multi-Exponential T2w dataĀ¶

https://mybinder.org/badge_logo.svg

Contents

% This m-file has been automatically generated using qMRgenBatch(mwf)
    % Command Line Interface (CLI) is well-suited for automatization
    % purposes and Octave.
    %
    % Please execute this m-file section by section to get familiar with batch
    % processing for mwf on CLI.
    %
    % Demo files are downloaded into mwf_data folder.
    %
    % Written by: Agah Karakuzu, 2017
    % =========================================================================
    

I- DESCRIPTION

qMRinfo('mwf'); % Describe the model
    
  mwf :  Myelin Water Fraction from Multi-Exponential T2w data

    Assumptions:

    Inputs:
    MET2data    Multi-Exponential T2 data
    (Mask)        Binary mask to accelerate the fitting (OPTIONAL)

    Outputs:
    MWF       Myelin Wanter Fraction
    T2MW      Spin relaxation time for Myelin Water (MW) [ms]
    T2IEW     Spin relaxation time for Intra/Extracellular Water (IEW) [ms]

    Options:
    Cutoff          Cutoff time [ms]
    Sigma           Noise standard deviation. Currently not corrected for rician bias
    Relaxation Type
    'T2'       For a SE sequence
    'T2*'      For a GRE sequence

    Protocol:
    MET2data   [TE1 TE2 ...] % list of echo times [ms]

    Example of command line usage:
    Model = mwf;  % Create class from model
    Model.Prot.MET2data.Mat=[10:10:320];
    data = struct;  % Create data structure
    data.MET2data ='MET2data.mat';  % Load data
    data.Mask = 'Mask.mat';
    FitResults = FitData(data,Model); %fit data
    FitResultsSave_mat(FitResults);

    For more examples: a href="matlab: qMRusage(mwf);"qMRusage(mwf)/a

    Author: Ian Gagnon, 2017

    References:
    Please cite the following if you use this module:
    MacKay, A., Whittall, K., Adler, J., Li, D., Paty, D., Graeb, D.,
    1994. In vivo visualization of myelin water in brain by magnetic
    resonance. Magn. Reson. Med. 31, 673?677.
    In addition to citing the package:
Karakuzu A., Boudreau M., Duval T.,Boshkovski T., Leppert I.R., Cabana J.F.,
Gagnon I., Beliveau P., Pike G.B., Cohen-Adad J., Stikov N. (2020), qMRLab:
Quantitative MRI analysis, under one umbrella doi: 10.21105/joss.02343

    Reference page in Doc Center
    doc mwf


    

II- MODEL PARAMETERS

a- create object

Model = mwf;
    

b- modify options

         |- This section will pop-up the options GUI. Close window to continue.
    |- Octave is not GUI compatible. Modify Model.options directly.
Model = Custom_OptionsGUI(Model); % You need to close GUI to move on.
    

III- FIT EXPERIMENTAL DATASET

a- load experimental data

         |- mwf object needs 2 data input(s) to be assigned:
    |-   MET2data
    |-   Mask
data = struct();

    % MET2data.mat contains [64  64   1  32] data.
    load('mwf_data/MET2data.mat');
    % Mask.mat contains [64  64] data.
    load('mwf_data/Mask.mat');
    data.MET2data= double(MET2data);
    data.Mask= double(Mask);
    

b- fit dataset

           |- This section will fit data.
FitResults = FitData(data,Model,0);
    
=============== qMRLab::Fit ======================
    Operation has been started: mwf
    Elapsed time is 0.060981 seconds.
    Operation has been completed: mwf
    ==================================================
    

c- show fitting results

         |- Output map will be displayed.
    |- If available, a graph will be displayed to show fitting in a voxel.
    |- To make documentation generation and our CI tests faster for this model,
    we used a subportion of the data (40X40X40) in our testing environment.
    |- Therefore, this example will use FitResults that comes with OSF data for display purposes.
    |- Users will get the whole dataset (384X336X224) and the script that uses it for demo
    via qMRgenBatch(qsm_sb) command.
FitResults_old = load('FitResults/FitResults.mat');
    qMRshowOutput(FitResults_old,data,Model);
    

d- Save results

         |-  qMR maps are saved in NIFTI and in a structure FitResults.mat
    that can be loaded in qMRLab graphical user interface
    |-  Model object stores all the options and protocol.
    It can be easily shared with collaborators to fit their
    own data or can be used for simulation.
FitResultsSave_nii(FitResults);
    Model.saveObj('mwf_Demo.qmrlab.mat');
    
Warning: Directory already exists.
    

V- SIMULATIONS

   |- This section can be executed to run simulations for mwf.

a- Single Voxel Curve

         |- Simulates Single Voxel curves:
    (1) use equation to generate synthetic MRI data
    (2) add rician noise
    (3) fit and plot curve
      x = struct;
    x.MWF = 50.0001;
    x.T2MW = 20.0001;
    x.T2IEW = 120;
    % Set simulation options
    Opt.SNR = 200;
    Opt.T2Spectrumvariance_Myelin = 5;
    Opt.T2Spectrumvariance_IEIntraExtracellularWater = 20;
    % run simulation
    figure('Name','Single Voxel Curve Simulation');
    FitResult = Model.Sim_Single_Voxel_Curve(x,Opt);
    

b- Sensitivity Analysis

         |-    Simulates sensitivity to fitted parameters:
    (1) vary fitting parameters from lower (lb) to upper (ub) bound.
    (2) run Sim_Single_Voxel_Curve Nofruns times
    (3) Compute mean and std across runs
      %              MWF           T2MW          T2IEW
    OptTable.st = [50            20            1.2e+02]; % nominal values
    OptTable.fx = [0             1             1]; %vary MWF...
    OptTable.lb = [0.0001        0.0001        40]; %...from 0.0001
    OptTable.ub = [1e+02         40            2e+02]; %...to 100
    % Set simulation options
    Opt.SNR = 200;
    Opt.T2Spectrumvariance_Myelin = 5;
    Opt.T2Spectrumvariance_IEIntraExtracellularWater = 20;
    Opt.Nofrun = 5;
    % run simulation
    SimResults = Model.Sim_Sensitivity_Analysis(OptTable,Opt);
    figure('Name','Sensitivity Analysis');
    SimVaryPlot(SimResults, 'MWF' ,'MWF' );