Modified the data load functions (io_loadspec_twix.m and related) so …

…that they write a field called out.seq, which contains information about the pulse sequence. In most cases this will not be used, but in some cases (ie. in the case of data acquired using WIP529), this information can be used by the functions or example run scripts. Specifically, I modified run_megapressproc.m so that it uses this information to determine how to properly combine the water unsuppressed sub-spectra. Thank you to Georg Oeltzschner, who spotted the problem and suggested the solutiongit status

exampleRunScripts/run_megapressproc.m

@@ -408,9 +408,15 @@
 out1_diff=op_combinesubspecs(out1,'diff');
 out1_sum=op_combinesubspecs(out1,'summ');
 
+
 %Make final water unsuppressed data
 if water
-    outw=op_combinesubspecs(outw_ls,'summ');
+    if strcmp(outw_ls.seq,'WIP529');
+        outw=op_combinesubspecs(outw_ls,'diff');
+    else
+        outw=op_combinesubspecs(outw_ls,'summ');
+    end
+    outw=op_addphase(outw,-phase(outw.fids(1))*180/pi,0,4.65,1);
 else
     outw=0;
 end

inputOutput/io_loadjmrui.m

@@ -50,6 +50,8 @@
 out.date=date;
 out.dims=dims;
 out.Bo=Bo;
+out.seq='';
+out.pointsToLeftshift=0;
 
 %Write flags
 out.flags.writtentostruct=1;

inputOutput/io_loadspec_GE.m

@@ -185,6 +185,7 @@
 out.rawAverages=rawAverages;
 out.subspecs=subspecs;
 out.rawSubspecs=rawSubspecs;
+out.seq='';
 out.pointsToLeftshift=0;
 
 
@@ -225,6 +226,7 @@
 out_w.rawAverages=rawAverages_w;
 out_w.subspecs=subspecs_w;
 out_w.rawSubspecs=rawSubspecs_w;
+out_w.seq='';
 out_w.pointsToLeftshift=0;
 
 

inputOutput/io_loadspec_IMA.m

@@ -163,6 +163,7 @@
 out.rawAverages=rawAverages;
 out.subspecs=subspecs;
 out.rawSubspecs=rawSubspecs;
+out.seq='';
 out.pointsToLeftshift=0;
 
 

inputOutput/io_loadspec_data.m

@@ -191,6 +191,7 @@
 out.rawAverages=rawAverages;
 out.subspecs=subspecs;
 out.rawSubspecs=rawSubspecs;
+out.seq='';
 out.pointsToLeftshift=0;
 
 
@@ -231,6 +232,7 @@
 out_w.rawAverages=rawAverages_w;
 out_w.subspecs=subspecs_w;
 out_w.rawSubspecs=rawSubspecs_w;
+out_w.seq='';
 out_w.pointsToLeftshift=0;
 
 

inputOutput/io_loadspec_sdat.m

@@ -153,6 +153,7 @@
 out.rawAverages=rawAverages;
 out.subspecs=subspecs;
 out.rawSubspecs=rawSubspecs;
+out.seq='';
 out.pointsToLeftshift=0;
 
 

inputOutput/io_loadspec_twix.m

@@ -63,6 +63,17 @@
     data=dOut.data;
 end
 
+%Make a pulse sequence identifier for the header (out.seq);
+if isSpecial
+    seq='rm_special'
+elseif isWIP529
+    seq='WIP529'
+else
+    seq='';
+end
+
+
+
 fids=squeeze(data);
 
 %If we are dealing with WIP 529, then we need to swap the order of the 
@@ -327,6 +338,7 @@
 out.rawAverages=rawAverages;
 out.subspecs=subspecs;
 out.rawSubspecs=rawSubspecs;
+out.seq=seq;
 if RaidLength==1
     out.pointsToLeftshift=twix_obj.image.freeParam(1);
 elseif RaidLength>1

inputOutput/io_loadspec_varian.m

@@ -111,6 +111,8 @@
 out.date=date;
 out.dims=dims;
 out.Bo=out.txfrq/42.577/1e6;
+out.seq='';
+out.pointsToLeftshift=0;
 
 %FILLING IN THE FLAGS
 out.flags.writtentostruct=1;

inputOutput/io_readlcmraw.m

@@ -163,6 +163,7 @@
 out.txfrq=txfrq;
 
 out.date=date;
+out.seq='';
 
 out.dims.t=1;
 out.dims.coils=0;

inputOutput/io_readlcmraw_basis.m

@@ -91,6 +91,7 @@
 out.txfrq=txfrq;
 
 out.date=date;
+out.seq='';
 
 out.dims.t=1;
 out.dims.coils=0;