Merge with develop branch

commit f979b85
Author: Jon-Fredrik Nielsen <jfnielse@umich.edu>
Date:   Wed Dec 6 13:30:20 2023 -0500

    Add usage of 'acqOrder' to help text
    On branch develop
    	modified:   loadpfile.m

commit 631e9f2
Author: Jon-Fredrik Nielsen <jfnielse@umich.edu>
Date:   Sat Dec 2 19:24:26 2023 -0500

    Change to conjugate phase
    On branch develop
    	modified:   slicesim.m

commit d623be4
Author: Jon-Fredrik Nielsen <jfnielse@umich.edu>
Date:   Sat Dec 2 17:21:33 2023 -0500

    More accurate RF center and refocusing area
    On branch develop
    	modified:   makeslr.m

On branch main
	modified:   +rf/makeslr.m
	modified:   +rf/slicesim.m
	modified:   loadpfile.m

+toppe/+utils/+rf/makeslr.m

@@ -281,12 +281,9 @@
 rf = [rf(:); zeros(mod(length(rf),2),1)];
 npix = length(rf);
 
-% find center (peak) of RF pulse. Smooth pulse first to reduce risk of picking an outlier
-I = find(rf==max(rf));              % approximate peak
-I = I(1);                           % in case length(I) > 1
-s = rf((I-20):(I+19));
-s = smooth(s);
-iref = find(s==max(s)) + I - 20;
+% find center (peak) of RF pulse
+I = find(abs(rf) > max(abs(rf(:)))-eps);
+iref= round(mean(I));
 
 %% make slice-select gradient waveform 
 bw = tbw / dur;                    % kHz
@@ -314,7 +311,7 @@
 % slice-select rephaser gradient
 switch type
 	case {'ex', 'st', 'sat'}
-		arearep = sum(gss_trap((iref):end)) * dt * 1e-3;            % G/cm*s
+		arearep = (gss_trap(iref)/2+sum(gss_trap((iref+1):end))) * dt * 1e-3;            % G/cm*s
 		gzrep = -trapwave2(arearep, mxg, spoilDerate*mxs, dt);
 	case 'se'
 		gzrep = [];

+toppe/+utils/+rf/slicesim.m

@@ -46,7 +46,7 @@
 nstep = length(rf);
 
 for ii = 1:length(Z)
-	Beff = [real(rf)*1e-4 imag(rf)*1e-4 Bz(:,ii)];                % [nstep 3], Tesla
+	Beff = [real(rf)*1e-4 -imag(rf)*1e-4 Bz(:,ii)];                % [nstep 3], Tesla
 	mtmp = toppe.utils.rf.blochsim(m0, Beff, T1, T2, dt, nstep);
 	m(ii) = mtmp(end,1) + 1i*mtmp(end,2);
 end

+toppe/+utils/loadpfile.m

@@ -12,6 +12,9 @@
 % Kwarg input options:
 %  acqOrder      true/false   If true, data is sorted in the order of acquisition. (default: false)
 %
+% To load data in order it was acquired, do:
+%    d = toppe.utils.loadpfile(pfile, [], [], [], 'acqOrder', true);
+%
 % Output dimensions of dat:
 %  [nFID, nc, nDabSlice, 1, maxView]