Merge pull request #1 from LarsonLab/HP_toolbox_edits

edits made in https://github.com/LarsonLab/hyperpolarized-mri-toolbox.git

create_freq_specs.m

@@ -1,15 +1,16 @@
-function [fspec, a_angs, d] = create_freq_specs(mets)
+function [fspec, a_angs, d] = create_freq_specs(mets, fmid)
 % CREATE_FREQ_SPECS - Helper function for creating spectral-spatial
 % frequency specifications
 %
-% [fspec, a_angs, d] = create_freq_specs(mets);
+% [fspec, a_angs, d] = create_freq_specs(mets, fmid);
 %   
 % INPUT
 %    mets - structure containing:
 %       mets(i).f - center frequency of bands (Hz)
 %       mets(i).df - bandwidth of bands (Hz)
 %       mets(i).ang - flip angle of bands (degress)
 %       mets(i).d - ripple of bands (Mxy, default = .01)
+%    fmid [optional] - center frequency spec around fmid
 %      
 % OUTPUT
 %    spec, a_angs, d - inputs for ss_design()
@@ -41,6 +42,9 @@
     end
 end
 
-% by default, center frequency specification 
-fmid = (mets(1).f+mets(end).f)/2; 
+if nargin < 2 || isempty(fmid)
+    % by default, center frequency specification 
+    fmid = (min(fspec)+max(fspec))/2; 
+end
+
 fspec = fspec - fmid;

examples/demo_C13_singleband.m

@@ -105,3 +105,49 @@
     ss_design(z_thk, z_tb, [z_d1 z_d2], fspec, a_angs, d, ptype, ...
 	      z_ftype, s_ftype, ss_type, fctr);
 set(gcf,'Name', '[1-13C]lac only for 14T animal system');
+
+fprintf(1,'Hit any key to continue:\n');
+pause;
+
+
+%% lactate-only pulse
+fprintf(1, '\nFor studies including copolarized 13C-urea or a 13C-urea phantom\n');
+fprintf(1, 'Here''s a C13 single-band excitation pulse to excite only [1-13C]lactate\n');
+fprintf(1, 'while not exciting pyruvate, alanine and pyruvate-hydrate AND urea, for a 3T clinical system\n\n');
+
+clear all; ss_opt([]);	ss_globals;			% Reset all options
+
+% GENERAL PULSE PARAMETERS
+ss_type = 'EP Whole';
+ptype = 'ex';  % excitation pulse
+opt = ss_opt({'Nucleus', 'Carbon', ...
+	      'Max Duration', 25e-3, ...
+          'Spect Correct', 1});
+
+% SPECTRAL PULSE PARAMETERS  - large pass/stop bands chosen for wide
+% supression regions
+B0 = 3e4; % G
+df = 0.5e-6 * B0 * SS_GAMMA; % 0.5 ppm = gamma_C13 * B0 * 0.5e-6
+% metabolite			frequency (Hz)		freq bandwidth (Hz)		flip angle (deg)
+mets(1).name = 'urea'; 	mets(1).f = -470; 	mets(1).df = 2*df;      mets(1).ang = 0; 
+mets(2).name = 'pyr'; 	mets(2).f = -230; 	mets(2).df = 2*df; 		mets(2).ang = 0; 
+mets(3).name = 'ala'; 	mets(3).f = -45; 	mets(3).df = 3*df;      mets(3).ang = 0; 
+mets(4).name = 'pyrh'; 	mets(4).f = 40; 	mets(4).df = 2*df; 		mets(4).ang = 0; 
+mets(5).name = 'lac'; 	mets(5).f = 165; 	mets(5).df = 2*df;      mets(5).ang = 90; 
+
+% create vectors of angles, ripples, and band edges for input to pulse design
+[fspec, a_angs, d] = create_freq_specs(mets);
+fctr = 0;  % force pulse design to optimize for center of frequency specification
+s_ftype = 'min';  % minimum-phase spectral filter
+
+% SPATIAL PULSE PARAMETERS
+z_thk = 1;  % thickness (cm)
+z_tb = 4; % time-bandwidth, proportional to profile sharpness
+z_ftype='ls';  % least-squares filter design
+z_d1 = 0.01;  z_d2 = 0.01;  % slice profile pass and stop-band ripples, respectively
+
+% DESIGN THE PULSE!
+[g,rf,fs,z,f,mxy] = ...
+    ss_design(z_thk, z_tb, [z_d1 z_d2], fspec, a_angs, d, ptype, ...
+	      z_ftype, s_ftype, ss_type, fctr);
+set(gcf,'Name', '[1-13C]lac only for 3T clinical system, avoiding urea');

ss_plot.m

@@ -227,7 +227,7 @@
 	subplot(4,nplot,3*nplot + idx);
 	m_f = calc_mag(rf_rot,gz_rot+i*gf_rot, z, fplot(idx),ptype);
     plot_mag(z,m_f,ptype);
-	title(sprintf('Spatial Profile - Freq = %5.1f', fplot(idx)));
+	title(sprintf('%5.1f', fplot(idx)));
 	xlabel('Position [cm]');
     end;