This directory in Jeff Fessler's Image reconstruction toolbox contains 
Matlab source code that computes spectral-spatial RF pulses (and the
corresponding z-gradient waveforms) for through-plane phase precompensatory
slice selection for T2*-weighted functional MRI.
This work is based on the publication: "Spectral-spatial RF pulse design for
through-plane phase precompensatory slice selection for T2*-weighted
functional MRI", Chun-yu Yip et al, Magnetic Resonance in Medicine, May, 2009.

SPSP pulse design source code:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
You should start by looking at the example in example_mri_rf_spsp.m
in the irt/mri-rf/spsp subdirectory of the toolbox.

The file is a central design script that will guide you through the whole
design process.  Remember: successful pulse design requires that the entire
image reconstruction toolbox by Jeff Fessler be installed first:

http://www.eecs.umich.edu/~fessler/code/index.html

You can conveniently download the whole package at
http://www.eecs.umich.edu/~fessler/irt/fessler.tgz
   
and use the unix command 'tar' to retrieve the files and folders.  In Matlab,
use the "setup.m" command in the toolbox to set up the paths first.

Ready-to-use SPSP pulse waveforms:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Alternatively, you can directly download the waveforms that I designed
and try them out on your MRI scanner:

http://www.eecs.umich.edu/~fessler/irt/irt/mri-rf/SPSPpulseset.mat

SPSPpulseset.mat is a Matlab workspace that contains SPSP pulses computed
with different "alpha" values based on our publication listed above.
It includes three kinds of variables:

1. gz           :real-value z gradient waveform (unit: Gauss/cm (g/cm))
2. b            :complex-value RF waveform (unit: g)
3. mresult      :complex-value Bloch simulation result (normalized)

In Matlab you can type "load SPSPpulseset.mat" to load the waveforms, and then
type "whos" to see all those variables.

The number(s) in each b or gz variable name indicate the "alpha" value (in
units of 1E-4 g/cm/Hz) for which the RF and z gradient waveforms were
computed, and each of the (b,gz) pairs leads to Bloch simulation result in
variable mresult with the same number(s).
Please refer to example_mri_rf_spsp.m for source code.
In the following we provide parameters with which the waveforms were computed
and the Bloch simulation was performed:

z gradient (gz)
~~~~~~~~~~~~~~~
sampling period = 4E-6 s
max gradient amplitude = 4 g/cm
max gradient slew rate = 15000 g/cm/s
oscillation period (T, in s) and number of trapezoids (Ntraps):

%   alpha=-1:   T = 0.0025;   Ntraps = 6;
%   alpha=-1.25:T = 0.0025;   Ntraps = 6;
%   alpha=-1.5: T = 0.0025;   Ntraps = 6;
%   alpha=-1.75:T = 0.0025;   Ntraps = 7;
%   alpha=-2:   T = 0.003;    Ntraps = 7;
%   alpha=-2.25:T = 0.003;    Ntraps = 7;
%   alpha=-2.5: T = 0.003;    Ntraps = 8;
%   alpha=-2.75:T = 0.003;    Ntraps = 8;
%   alpha=-3:   T = 0.003;    Ntraps = 9;
%   alpha=-3.25:T = 0.003;    Ntraps = 10;
%   alpha=-3.5: T = 0.003;    Ntraps = 10;
                                
RF pulse (b)
~~~~~~~~~~~~
sampling period = 4E-6 s
slice thickness = 0.5 cm
flip angle = 30 degrees
slice profile = 'rectangular'
desired pattern specifications:
	range in z (space) = 20 cm
	number of samples in z = 1200
	range in f (frequency) = 500 Hz
	number of samples in f = 300
zshift = -0.25 m
alpha = indicated in variable name, in units of 1E-4 g/cm/Hz
TE = 30 ms
conjugate gradient:
	number of iterations = 100
	beta (Tikhonov regularization) = 0

Bloch simulation (mresult)
~~~~~~~~~~~~~~~~~~~~~~~~~
range in z (space) = 3 cm
number of samples in z = 200
range in f (frequency) = 500 Hz
number of samples in f = 200


Thank you for your interest in our spectral-spatial pulses.
Written by Chun-yu Yip, University of Michigan, Ann Arbor, 4/1/2009
Please contact Chun-yu Yip if you have questions or problems. Enjoy!
Current email: YIP_chun_yu@sbic.a-star.edu.sg

Jeff Fessler made minor modifications to several of the files.
Hopefully I did not break anything...