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% This m-file has been automatically generated using qMRgenBatch(qmt_bssfp)% 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 qmt_bssfp on CLI.%% Demo files are downloaded into qmt_bssfp_data folder.%% Written by: Agah Karakuzu, 2017% =========================================================================
I- DESCRIPTION
qMRinfo('qmt_bssfp'); % Describe the model
qmt_bssfp : qMT using Balanced Steady State Free Precession acquisition
-----------------------------------------------------------------------------------------------------
Assumptions:
Inputs:
MTdata 4D Magnetization Transfer data
(R1map) 1/T1map (optional)
(Mask) Binary mask to accelerate the fitting (optional)
Outputs:
F Ratio of number of restricted pool to free pool, defined
as F = M0r/M0f = kf/kr.
kr Exchange rate from the free to the restricted pool
(note that kf and kr are related to one another via the
definition of F. Changing the value of kf will change kr
accordingly, and vice versa).
R1f Longitudinal relaxation rate of the free pool
(R1f = 1/T1f).
R1r Longitudinal relaxation rate of the restricted pool
(R1r = 1/T1r).
T2f Tranverse relaxation time of the free pool (T2f = 1/R2f).
M0f Equilibrium value of the free pool longitudinal
magnetization.
Additional Outputs
M0r Equilibrium value of the restricted pool longitudinal
magnetization.
kf Exchange rate from the restricted to the free pool.
resnorm Fitting residual.
Protocol:
MTdata Array [nbVols x 2]:
Alpha Flip angle of the RF pulses (degrees)
Trf Duration of the RF pulses (s)
Options:
RF Pulse
Shape Shape of the RF pulses.
Available shapes are:
- hard
- gaussian
- gausshann (gaussian pulse with Hanning window)
- sinc
- sinchann (sinc pulse with Hanning window)
- singauss (sinc pulse with gaussian window)
- fermi
Nb of RF pulses Number of RF pulses applied before readout.
Protocol Timing
Fix TR Select this option and enter a value in the text
box below to set a fixed repetition time.
Fix TR - Trf Select this option and enter a value in the text
box below to set a fixed free precession time
(TR - Trf).
Prepulse Perform an Alpha/2 - TR/2 prepulse before each
series of RF pulses.
R1
Use R1map to By checking this box, you tell the fitting
constrain R1f algorithm to check for an observed R1map and use
its value to constrain R1f. Checking this box
will automatically set the R1f fix box to true in
the Fit parameters table.
Fix R1r = R1f By checking this box, you tell the fitting
algorithm to fix R1r equal to R1f. Checking this
box will automatically set the R1r fix box to
true in the Fit parameters table.
Global
G(0) The assumed value of the absorption lineshape of
the restricted pool.
References:
Please cite the following if you use this module:
In addition to citing the package:
Cabana J-F, Gu Y, Boudreau M, Levesque IR, Atchia Y, Sled JG, Narayanan S, Arnold DL, Pike GB, Cohen-Adad J, Duval T, Vuong M-T and Stikov N. (2016), Quantitative magnetization transfer imaging made easy with qMTLab: Software for data simulation, analysis, and visualization. Concepts Magn. Reson.. doi: 10.1002/cmr.a.21357
Reference page in Doc Center
doc qmt_bssfp
II- MODEL PARAMETERS
a- create object
Model = qmt_bssfp;
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
|- qmt_bssfp object needs 3 data input(s) to be assigned:
|- MTdata
|- R1map
|- Mask
|- 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.
|- 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.
|- 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
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