I- DESCRIPTION

In [ ]:
qMRinfo('mt_sat'); % Describe the model

II- MODEL PARAMETERS

a- Create object

In [ ]:
Model = mt_sat;

Download sample data from OSF

The current Model is an instance of mt_sat class.

You can manually download the sample data for mt_sat by clicking here.

In [ ]:
dataDir = downloadData(Model,pwd);

b- Set protocol

Protocol is set according to the example data

% |- mt_sat object needs 3 protocol field(s) to be assigned: % |- MTw % |- T1w % |- PDw

In [ ]:
FlipAngle = 6;
TR  = 0.028;
Model.Prot.MTw.Mat = [ FlipAngle TR ];
%%   
FlipAngle = 20;
TR = 0.018;
Model.Prot.T1w.Mat = [ FlipAngle TR];
%%   
FlipAngle = 6;
TR = 0.028;
Model.Prot.PDw.Mat = [ FlipAngle TR];
%%

III- FIT EXPERIMENTAL DATASET

a- Load experimental data

% |- mt_sat object needs 5 data input(s) to be assigned: % |- MTw % |- T1w % |- PDw % |- B1map % |- Mask

In [ ]:
% MTw.nii.gz contains [128  128   96] data.
data.MTw=double(load_nii_data('mt_sat_data/MTw.nii.gz'));
% T1w.nii.gz contains [128  128   96] data.
data.T1w=double(load_nii_data('mt_sat_data/T1w.nii.gz'));
% PDw.nii.gz contains [128  128   96] data.
data.PDw=double(load_nii_data('mt_sat_data/PDw.nii.gz'));

b- Fit experimental data

This section will fit data.

In [ ]:
FitResults = FitData(data,Model,0);

c- Show fitting results

  • Output map will be displayed.

  • If available, a graph will be displayed to show fitting in a voxel.

In [ ]:
qMRshowOutput(FitResults,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
  • These objects can be easily shared or be used for simulation.
In [ ]:
FitResultsSave_nii(FitResults, 'mt_sat_data/MTw.nii.gz');