8000 [FEATURE] - XA30 loader Siemens WIP MEGA - load_twix - gunziyhu by HJZollner · Pull Request #503 · schorschinho/osprey · GitHub
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[FEATURE] - XA30 loader Siemens WIP MEGA - load_twix - gunziyhu #503

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Merged
merged 1 commit into from
Aug 18, 2022
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[FEATURE] - XA30 loader Siemens WIP MEGA - load_twix - gunziyhu #503

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4 changes: 2 additions & 2 deletions fit/osp_fitMEGA.m
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@
% Apply scaling factor to the data
dataToFit = op_takesubspec(MRSCont.processed.metab{kk},'A');
basisSetOff = MRSCont.fit.basisSet;
basisSetOff.name{1} = 'A';
basisSetOff.names{1} = 'A';
basisSetOff.fids = basisSetOff.fids(:,:,1);
basisSetOff.specs = basisSetOff.specs(:,:,1);
dataToFit = op_ampScale(dataToFit, 1/MRSCont.fit.scale{kk});
Expand Down Expand Up @@ -103,7 +103,7 @@
end

fitOpts.GAP = MRSCont.opts.fit.GAP.diff1;
basisSetDiff1.name{1} = 'diff1';
basisSetDiff1.names{1} = 'diff1';
% Call the fit function
[fitParamsDiff1, resBasisSetDiff1] = fit_runFit(dataToFit, basisSetDiff1, fitModel, fitOpts);

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32 changes: 22 additions & 10 deletions libraries/FID-A/inputOutput/io_loadspec_twix.m
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Original file line number Diff line number Diff line change
Expand Up @@ -48,10 +48,13 @@

%Check if the twix file is from a VE version
if contains(twix_obj.hdr.Dicom.SoftwareVersions, 'E11')
disp('Changed software version to VE.');
twix_obj.image.softwareVersion = 've';
version=twix_obj.image.softwareVersion;
end
if contains(twix_obj.hdr.Dicom.SoftwareVersions, 'XA30')
twix_obj.image.softwareVersion = 'XA30';
version=twix_obj.image.softwareVersion;
end

%find out what sequence, the data were acquired with. If this is a
%multi-raid file, then the header may contain multiple instances of
Expand Down Expand Up @@ -90,10 +93,13 @@
elseif isUniversal
if twix_obj.hdr.MeasYaps.sWipMemBlock.alFree{8} == 1
seq = 'HERMES';
else if isempty(twix_obj.hdr.MeasYaps.sWipMemBlock.alFree{8})
seq = 'MEGAPRESS';
else
else if twix_obj.hdr.MeasYaps.sWipMemBlock.alFree{8} == 3
seq = 'HERCULES';
else if isempty(twix_obj.hdr.MeasYaps.sWipMemBlock.alFree{8})
seq = 'MEGAPRESS';
else
seq = 'HERCULES';
end
end
end
elseif isMinn
Expand Down Expand Up @@ -134,8 +140,8 @@
%25 Oct 2018: Due to a recent change, the VE version of Jamie Near's MEGA-PRESS
%sequence also falls into this category.
if isSpecial ||... %Catches Ralf Mekle's and CIBM version of the SPECIAL sequence
((strcmp(version,'vd') || strcmp(version,'ve')) && isjnSpecial) ||... %and the VD/VE versions of Jamie Near's SPECIAL sequence
((strcmp(version,'vd') || strcmp(version,'ve')) && isjnMP); %and the VD/VE versions of Jamie Near's MEGA-PRESS sequence
((strcmp(version,'vd') || strcmp(version,'ve') || strcmp(version,'XA30')) && isjnSpecial) ||... %and the VD/VE versions of Jamie Near's SPECIAL sequence
((strcmp(version,'vd') || strcmp(version,'ve') || strcmp(version,'XA30')) && isjnMP); %and the VD/VE versions of Jamie Near's MEGA-PRESS sequence
squeezedData=squeeze(dOut.data);
if twix_obj.image.NCol>1 && twix_obj.image.NCha>1
data(:,:,:,1)=squeezedData(:,:,[1:2:end-1]);
Expand Down Expand Up @@ -180,7 +186,7 @@

%noticed that in the Siemens PRESS and STEAM sequences, there is sometimes
%an extra dimension containing unwanted reference scans or something. Remove them here.
if isSiemens && (strcmp(version,'vd') || strcmp(version,'ve')) && strcmp(sqzDims{end},'Phs')
if isSiemens && (strcmp(version,'vd') || strcmp(version,'ve') || strcmp(version,'XA30')) && strcmp(sqzDims{end},'Phs')
sqzDims=sqzDims(1:end-1);
sqzSize=sqzSize(1:end-1);
if ndims(fids)==4
Expand Down Expand Up @@ -215,7 +221,7 @@
TR = twix_obj.hdr.MeasYaps.alTR{1}; %Franck Lamberton

% Extract voxel dimensions
if (strcmp(version,'vd') || strcmp(version,'vb'))
if (strcmp(version,'vd') || strcmp(version,'vb') || strcmp(version,'XA30'))
TwixHeader.VoI_RoFOV = twix_obj.hdr.Config.VoI_RoFOV; % Voxel size in readout direction [mm]
TwixHeader.VoI_PeFOV = twix_obj.hdr.Config.VoI_PeFOV; % Voxel size in phase encoding direction [mm]
TwixHeader.VoIThickness = twix_obj.hdr.Config.VoI_SliceThickness; % Voxel size in slice selection direction [mm]
Expand Down Expand Up @@ -292,7 +298,7 @@
end

%Now index the dimension of the averages
if strcmp(version,'vd') || strcmp(version,'ve')
if strcmp(version,'vd') || strcmp(version,'ve') || strcmp(version,'XA30')
if isMinn || isConnectom
dims.averages=find(strcmp(sqzDims,'Set'));
else
Expand Down Expand Up @@ -338,8 +344,14 @@
else
dims.subSpecs=find(strcmp(sqzDims,'Ida'));
end
elseif isWIP529 || isMinn || ismodWIP
elseif isWIP529 || isMinn
dims.subSpecs=find(strcmp(sqzDims,'Eco'));
elseif ismodWIP
if strcmp(version,'vd') || strcmp(version,'ve')
dims.subSpecs=find(strcmp(sqzDims,'Eco'));
else
dims.subSpecs=find(strcmp(sqzDims,'Ide'));
end
elseif isWIP859
dims.subSpecs=find(strcmp(sqzDims,'Ide'));
else
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