qsm_sb: Fast quantitative susceptibility mapping



% This m-file has been automatically generated using qMRgenBatch(qsm_sb)
    % 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 qsm_sb on CLI.
    % Demo files are downloaded into qsm_sb_data folder.
    % Written by: Agah Karakuzu, 2017
    % =========================================================================


qMRinfo('qsm_sb'); % Describe the model
  qsm_sb: Compute a T1 map using Variable Flip Angle

    Type/number of outputs will depend on the selected options.
    (1) Case - Split-Bregman:
    i)  W/ magnitude weighting:  chiSBM, chiL2M, chiL2, unwrappedPhase, maskOut
    ii) W/O magnitude weighting: chiSM, chiL2, unwrappedPhase, maskOut
    (2) Case - L2 Regularization:
    i)  W/ magnitude weighting:  chiL2M, chiL2, unwrappedPhase, maskOut
    ii) W/O magnitude weighting: chiL2, unwrappedPhase, maskOut
    (3) Case - No Regularization:
    i) Magnitude weighting is not enabled: nfm, unwrappedPhase, maskOut
    PhaseGRE      3D GRE acquisition. Wrapped phase image
    (MagnGRE)     3D GRE acquisition. Magnitude part of the image
    Mask          Brain extraction mask.

    chiSBM          Susceptibility map created using Split-Bregman method with magnitude weighting
    chiSB           Susceptibility map created using Split-Bregman method without magnitude weighting.
    chiL2M          Susceptibility map created using L2 regularization with magnitude weighting
    chiL2           Susceptibility map created using L2 regularization without magnitude weighting
    nfm             Susceptibility map created without regularization
    unwrappedPhase  Unwrapped phase image using Laplacian-based method
    maskOut         Binary mask (maskSharp, gradientMask or same as the input)

    Derivative direction               Direction of the derivation
    - forward
    - backward
    SHARP Filtering                    Sophisticated harmonic artifact reduction for phase data
    - State: true/false
    - Mode: once/iterative
    - Padding Size: [1X3 array]
    - Magnitude Weighting: on/off
    L1-Regularization                  Apply L1-regularization
    - State: true/false
    - Reoptimize parameters:
    - Lambda-L1: [double]
    - L1-Range:  [1X2 array]
    L2-Regularization                  Apply L2-regularization
    - State: true/false
    - Reoptimize parameters:
    - Lambda-L2: [double]
    - L2-Range:  [1X2 array]
    Split-Bregman                       Apply Split-Bregman method
    - State: true/false
    - Reoptimize parameters:

    Authors: Agah Karakuzu, 2018

    Please cite the following if you use this module:
    Bilgic et al. (2014), Fast quantitative susceptibility mapping with
    L1-regularization and automatic parameter selection. Magn. Reson. Med.,
    72: 1444-1459. doi:10.1002/mrm.25029
    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 qsm_sb



a- create object

Model = qsm_sb;

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.


a- load experimental data

         |- qsm_sb object needs 3 data input(s) to be assigned:
    |-   PhaseGRE
    |-   MagnGRE
    |-   Mask
data = struct();

    % PhaseGRE.mat contains [40  40  40] data.
    % MagnGRE.mat contains [40  40  40] data.
    % Mask.mat contains [40  40  40] data.
    data.PhaseGRE= double(PhaseGRE);
    data.MagnGRE= double(MagnGRE);
    data.Mask= double(Mask);

b- fit dataset

           |- This section will fit data.
FitResults = FitData(data,Model,0);
=============== qMRLab::Fit ======================
    Operation has been started: qsm_sb
    Started   : Laplacian phase unwrapping ...
    Completed : Laplacian phase unwrapping
    Started   : SHARP background removal ...
    Completed : SHARP background removal
    Skipping reoptimization of Lambda L2.
    Started   : Calculation of chi_L2 map without magnitude weighting...
    Elapsed time is 0.016576 seconds.
    Completed  : Calculation of chi_L2 map without magnitude weighting.
    Started   : Calculation of chi_SB map without magnitude weighting.. ...
    Iteration  1  -  Change in Chi: 100 %
    Iteration  2  -  Change in Chi: 28.2724 %
    Iteration  3  -  Change in Chi: 14.6621 %
    Iteration  4  -  Change in Chi: 10.3776 %
    Iteration  5  -  Change in Chi: 6.7868 %
    Iteration  6  -  Change in Chi: 4.9906 %
    Iteration  7  -  Change in Chi: 3.7381 %
    Iteration  8  -  Change in Chi: 2.8073 %
    Iteration  9  -  Change in Chi: 2.3136 %
    Iteration  10  -  Change in Chi: 1.9299 %
    Iteration  11  -  Change in Chi: 1.6742 %
    Iteration  12  -  Change in Chi: 1.4638 %
    Iteration  13  -  Change in Chi: 1.2977 %
    Iteration  14  -  Change in Chi: 1.1512 %
    Iteration  15  -  Change in Chi: 1.0556 %
    Iteration  16  -  Change in Chi: 0.96335 %
    Elapsed time is 1.657627 seconds.
    Elapsed time is 1.678697 seconds.
    Completed   : Calculation of chi_SB map without magnitude weighting.
    Loading outputs to the GUI may take some time after fit has been completed.
    Elapsed time is 1.701097 seconds.
    Operation has been completed: qsm_sb

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');

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.
Warning: Directory already exists.


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

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
% Not available for the current model.

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
% Not available for the current model.