Merge branch 'develop' of github.com:toppeMRI/toppe into develop

+toppe/+utils/getk.m

@@ -0,0 +1,26 @@
+function [kxo, kxe] = getk(sysGE, readoutFile, nfid, del)
+% Get kspace sample locations from .mod file
+% 
+% Inputs:
+%  sysGE          see toppe.systemspecs()
+%  readoutFile    .mod file name containing ADC window
+%  nfid           number of acquired samples in ADC window
+%
+% Option:
+%  del            offset by this many samples (default: 0)
+%
+% Outputs:
+%  kxo            [1 nfid], odd echo k-space, cycles/cm
+%  kxe            [1 nfid], even echo k-space, cycles/cm
+
+if nargin < 4
+    del = 0.0;
+end
+
+[rf,gx,gy,gz,desc,paramsint16,paramsfloat,hdr] = toppe.readmod(readoutFile);
+kx = sysGE.raster*1e-6*sysGE.gamma*1e-4*cumsum(gx);  % cycles/cm
+kx = kx - kx(end)/2;
+kx = kx((hdr.npre+1):(hdr.npre+nfid));
+kxo = interp1(1:nfid, kx, (1:nfid) - 0.5 - del, 'linear', 'extrap');
+kxe = interp1(1:nfid, kx, (1:nfid) + 0.5 + del, 'linear', 'extrap');
+kxe = fliplr(kxe);

+toppe/plotseq.m

@@ -298,7 +298,6 @@
 
     p = loop(n,1);   % module id
     w = loop(n,16);  % waveform index
-
     dur = 0;
 
     % Pure delay block
@@ -330,7 +329,7 @@
 
     % Calculate RF and gradient waveforms for this block
     rho1 = [ia_rf/max_pg_iamp*abs(modules{p}.rf(:,w))];
-    th1 = [ia_rf/max_pg_iamp*angle(modules{p}.rf(:,w))];
+    th1 = angle(modules{p}.rf(:,w));
     gxit = ia_gx/max_pg_iamp*modules{p}.gx(:,w);
     gyit = ia_gy/max_pg_iamp*modules{p}.gy(:,w);
     gzit = ia_gz/max_pg_iamp*modules{p}.gz(:,w);

+toppe/preflightcheck.m

@@ -69,7 +69,7 @@ function preflightcheck(entryFile, seqstampFile, sysGE)
 modArr = toppe.tryread(@toppe.readmodulelistfile, moduleListFile);
 
 % Check that:
-%  - all .mod files use the same peak RF limit (e.g., 0.25 Gauss)
+%  - b1CheckFile represents the RF pulse with peak RF amplitude across the whole the sequence
 %  - all .mod files used to acquire data have the same number of ADC samples as readoutFilterFile.
 [~,~,~,~,~,~,~,hdr] = toppe.readmod(b1CheckFile);
 b1limit = hdr.b1max;
@@ -82,8 +82,8 @@ function preflightcheck(entryFile, seqstampFile, sysGE)
         error(sprintf('Number of samples in %s and %s do not match (must be same across all .mod files containing ADC windows)', ...
             readoutFilterFile, modArr{ii}.fname));
     end
-    if hdr.b1max ~= b1limit 
-        error(sprintf('B1 limit in %s does not match %s (must be the same across all .mod files)', ...
+    if modArr{ii}.hasRF & hdr.b1max > b1limit 
+        error(sprintf('Peak B1 limit in %s cannot exceed the b1 scaling .mod file in %s', ...
             modArr{ii}.fname, entryFile));
     end
 end
@@ -196,7 +196,7 @@ function preflightcheck(entryFile, seqstampFile, sysGE)
 fprintf(fout, '%.4f\n', max(abs(rf)));  % needed to scale max_seqsar in .e file
 fprintf(fout, '%.4f\n', gmax);          % max gradient across all .mod files (Gauss)
 fprintf(fout, '%.4f\n', slewmax);       % max slew across all .mod files (G/cm/ms)
-fprintf(fout, '%.4f\n', b1limit);       % hardware b1 limit (Gauss) 
+fprintf(fout, '%.4f\n', b1limit);       % peak B1 in sequence (Gauss)
 
 fclose(fout);
 

+toppe/writemod.m

@@ -144,7 +144,8 @@ function writemod(sysGE, varargin)
 dtycyc        = length(find(abs(b1)>0.2236*max(abs(b1)))) / length(b1);
 maxpw         = dtycyc;
 num           = 1;
-max_b1        = sysGE.maxRF;                       	% Gauss. Full instruction amplitude (32766) should produce max_b1 RF amplitude,
+max_b1        = sysGE.maxRF;        % Gauss. Full instruction amplitude (32766) should produce max_b1 RF amplitude,
+%max_b1        = max(abs(b1(:)));     % Gauss
 																		% as long as other RF .mod files (if any) use the same max_b1.
 max_int_b1_sq = max( cumsum(abs(b1).^2)*dt*1e3 );   	% Gauss^2 - ms
 max_rms_b1    = sqrt(mean(abs(b1).^2));              	% Gauss