Merge pull request #685 from HJZollner/develop

[FEATURE] - Support CMRR sequence with integrated water refernece
schorschinho · Dec 21, 2023 · 78a7f89 · 78a7f89
2 parents 637b340 + 8d65313
commit 78a7f89
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Showing 3 changed files with 18 additions and 2 deletions.
diff --git a/load/osp_LoadTwix.m b/load/osp_LoadTwix.m
@@ -63,14 +63,26 @@
         if ~(MRSCont.flags.didLoad == 1 && MRSCont.flags.speedUp && isfield(MRSCont, 'raw') && (kk > length(MRSCont.raw))) || ~strcmp(MRSCont.ver.Osp,MRSCont.ver.CheckOsp)
             % Read in the raw metabolite data
             metab_ll = MRSCont.opts.MultipleSpectra.metab(ll);
-            raw                         = io_loadspec_twix(MRSCont.files{metab_ll,kk});
+            [raw, raw_ref]              = io_loadspec_twix(MRSCont.files{metab_ll,kk});
             raw                         = op_leftshift(raw,raw.pointsToLeftshift);
+            if ~isempty(raw_ref)
+                raw_ref                 = op_leftshift(raw_ref,raw_ref.pointsToLeftshift);
+                ref_ll                  = MRSCont.opts.MultipleSpectra.metab(ll);       
+                MRSCont.opts.MultipleSpectra.ref(ll)    = MRSCont.opts.MultipleSpectra.metab(ll);    
+            end
             if strcmp(raw.seq,'SLASER_D')
                 raw = op_truncate(raw,2068,0);
+                if ~isempty(raw_ref)
+                    raw_ref                 = op_leftshift(raw_ref,raw_ref.pointsToLeftshift);
+                end
             end
             % Add NIfTI-MRS information
             raw                           = osp_add_nii_mrs_field(raw,MRSCont.ver.Osp);
             MRSCont.raw_uncomb{ll,kk}      = raw;
+            if ~isempty(raw_ref)
+                raw_ref                        = osp_add_nii_mrs_field(raw_ref,MRSCont.ver.Osp);
+                MRSCont.raw_ref_uncomb{ll,kk}  = raw_ref;
+            end
             % Read in the raw reference data. If a reference exists, perform the
             % coil combination based on the reference, and perform an eddy current
             % correction. If not, combine metabolite data based on its own signal.
@@ -83,6 +95,9 @@
                 MRSCont.raw_ref_uncomb{ref_ll,kk}  = raw_ref;
             else
                 ref_ll = 1;
+                if ~isempty(raw_ref)
+                    MRSCont.flags.hasRef = 1;
+                end
             end
             if MRSCont.flags.hasWater
                 w_ll = MRSCont.opts.MultipleSpectra.w(ll);

diff --git a/plot/osp_plotLoad.m b/plot/osp_plotLoad.m
@@ -70,7 +70,7 @@
                         [~,filen,ext] = fileparts(MRSCont.files_mm{ExpIndex,kk});% re_mm
                         figTitle = sprintf(['Load MM data plot: ' filen ext '\n']);% re_mm
                 case 'ref'
-                    if ~(strcmp(MRSCont.datatype,'P') || strcmp(MRSCont.datatype,'DATA'))
+                    if ~(strcmp(MRSCont.datatype,'P') || strcmp(MRSCont.datatype,'DATA') || isempty(MRSCont.files_ref))
                         [~,filen,ext] = fileparts(MRSCont.files_ref{ExpIndex,kk});
                         figTitle = sprintf(['Load water reference data plot: ' filen ext '\n']);
                     else

diff --git a/process/osp_combineCoils.m b/process/osp_combineCoils.m
@@ -90,6 +90,7 @@
                     else
                         cweights_w          = op_getcoilcombos(MRSCont.raw_w_uncomb{w_ll,kk}, 1, 'h');
                     end
+                    cweights_w.ref      = 'raw_w';
                     raw_w_comb          = op_addrcvrs(MRSCont.raw_w_uncomb{w_ll,kk},1,'h',cweights_w);
                     raw_w_comb.flags.isUnEdited = 1;
                     MRSCont.raw_w{w_ll,kk}   = raw_w_comb;