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Develop #1

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afea324
Merge branch 'develop'
Jun 17, 2022
2a07463
combines fat excitation and spoiling, adds fatsatmod to scanloop
masalifu Jul 30, 2022
a973884
Combines fat excitation and spoiling, adds fatsatmod to scanlooop
masalifu Jul 30, 2022
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33 changes: 21 additions & 12 deletions b0/GE/b04ge.m
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Original file line number Diff line number Diff line change
Expand Up @@ -41,17 +41,17 @@ function b04ge(sys, N, FOV, flip, DTE, varargin)
% substitute with provided keyword arguments
arg = toppe.utils.vararg_pair(arg, varargin);

nScans = numel(DTE);
% nScans = numel(DTE);

% Since we are using the helper function 'makegre' below,
% the in-plane FOV and matrix size must be square.
if N(1) ~= N(2) | FOV(1) ~= FOV(2)
if N(1) ~= N(2) || FOV(1) ~= FOV(2)
error('In-plane FOV and matrix be square.');
end

voxSize = FOV./N; % cm

ny = N(2);
% ny = N(2);
nz = N(3);

% Write modules.txt
Expand All @@ -76,7 +76,7 @@ function b04ge(sys, N, FOV, flip, DTE, varargin)


%% Create .mod files

if arg.fatsat
% fat sat module (including spoiler)
fatsat.flip = 90;
fatsat.slThick = 1000; % dummy value (determines slice-select gradient, but we won't use it; just needs to be large to reduce dead time before+after rf pulse)
Expand All @@ -87,24 +87,27 @@ function b04ge(sys, N, FOV, flip, DTE, varargin)
b1 = toppe.utils.rf.makeslr(fatsat.flip, fatsat.slThick, fatsat.tbw, fatsat.dur, 1e-6, sys, ...
'type', 'ex', ... % fatsat pulse is a 90 so is of type 'ex', not 'st' (small-tip)
'writeModFile', false);
b1 = toppe.makeGElength(b1);
toppe.writemod(sys, 'rf', b1, 'ofname', 'fatsat.mod', 'desc', 'fat sat pulse');

%% Spoiler
%Spoiler for fatsat
tmpslew = 6; % G/cm/ms
gspoil = toppe.utils.makecrusher(2, 0.3, sys, 0, tmpslew); % 2 cycles of spoiling across 0.3 cm
gspoil = toppe.makeGElength(gspoil);
toppe.writemod(sys, 'gx', gspoil, ... % tipdown.mod already has spoiler on z
'ofname', 'spoiler.mod', 'desc', 'gradient spoiler');

% excitation module
%combining fat excitation and spoiling to make a fatsat mod
gspoil =[0*b1; gspoil];
b1 = [b1;0*gspoil];
gspoil= toppe.makeGElength(gspoil);
b1 = toppe.makeGElength(b1);
toppe.writemod(sys, 'rf', b1, 'gz', gspoil, 'ofname', 'fatsat.mod');
end

% excitation module for B0
[ex.rf, ex.g] = toppe.utils.rf.makeslr(flip, arg.slabThick, ...
arg.tbw, arg.rfDur, nz*arg.nCyclesSpoil, sys, ...
'ftype', arg.ftype, ...
'spoilDerate', 0.5, ...
'ofname', arg.exMod);

% readout module
% readout module for B0
% Here we use the helper function 'makegre' to do that, but
% that's not a requirement.
% Reduce slew to keep PNS in normal mode (<80% of limit)
Expand All @@ -129,6 +132,12 @@ function b04ge(sys, N, FOV, flip, DTE, varargin)
% My convention is to start at (-kymax, -kzmax)
a_gy = -((iy-1+0.5)-ny/2)/(ny/2) * (iz>0);
a_gz = -((iz-1+0.5)-nz/2)/(nz/2) * (iz>0);

if arg.fatsat
toppe.write2loop('fatsat.mod', sys, ...
'Gamplitude', [0 0 1]', ...
'RFoffset', fatsat.freq);
end

toppe.write2loop(arg.exMod, sys, ...
'RFamplitude', 1.0, ...
Expand Down