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[BUG FIX] - 180 flip not corrected before alignment - OspreyProcess -…
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… Several reports

- New PreservePolarity flag was not implemented correctly. Therefore, not all datasets were polarity corrected before the spectral alignment.
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@HJZollner
HJZollner committed Jul 15, 2024
1 parent 5e4d4c0 commit 9a59837
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Showing 4 changed files with 32 additions and 25 deletions.
2 changes: 1 addition & 1 deletion GUI/osp_Toolbox_Check.m
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Expand Up @@ -32,7 +32,7 @@
% 2020-05-15: First version of the code.
%% % 1. SAVE OSPREY VERSION%%%
%%% 1. SAVE OSPREY VERSION%%%
OspreyVersion = 'Osprey 2.4.0';
OspreyVersion = 'Osprey 2.5.0';
fprintf(['Timestamp %s ' OspreyVersion ' ' Module '\n'], datestr(now,'mmmm dd, yyyy HH:MM:SS'));
hasSPM = 1; % For the compiled GUI
%% % 2. GET SPMPATH AND TOOLBOXES%%%
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16 changes: 11 additions & 5 deletions libraries/FID-A/inputOutput/io_loadspec_sdat.m
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Expand Up @@ -26,11 +26,15 @@
% OUTPUTS:
% out = Input dataset in FID-A structure format.

function out = io_loadspec_sdat(filename,subspecs,series)
function out = io_loadspec_sdat(filename,subspecs,series,undoPhaseCycle)

if nargin<3
series = 0;
if nargin<4
undoPhaseCycle = 1;
if nargin<3
series = 0;
end
end

% Read in the data and header information
[data, header] = philipsLoad(filename);

Expand Down Expand Up @@ -80,8 +84,10 @@
% according to the 'subspecs' input.
% Initialize fids array:
fids = squeeze(zeros(header.samples, header.rows/subspecs, subspecs));
% Remove phase cycle
fids = fids .* repmat(conj(fids(1,:,:,:))./abs(fids(1,:,:,:)),[size(fids,1) 1]);
if undoPhaseCycle
% Remove phase cycle
fids = fids .* repmat(conj(fids(1,:,:,:))./abs(fids(1,:,:,:)),[size(fids,1) 1]);
end
if subspecs == 2
%Split the subspectra out of the "averages" dimension:
fids(:,:,1) = data(:,[1:2:end]);
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36 changes: 18 additions & 18 deletions load/osp_LoadSDAT.m
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Expand Up @@ -71,16 +71,16 @@
% type of sequence needs to be differentiated here already.
metab_ll = MRSCont.opts.MultipleSpectra.metab(ll);
if MRSCont.flags.isUnEdited
raw = io_loadspec_sdat(MRSCont.files{metab_ll,kk},1,MRSCont.flags.isSERIES);
raw = io_loadspec_sdat(MRSCont.files{metab_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw.flags.isUnEdited = 1;
elseif MRSCont.flags.isMEGA
raw = io_loadspec_sdat(MRSCont.files{metab_ll,kk},2,MRSCont.flags.isSERIES);
raw = io_loadspec_sdat(MRSCont.files{metab_ll,kk},2,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw.flags.isMEGA = 1;
elseif MRSCont.flags.isHERMES
raw = io_loadspec_sdat(MRSCont.files{metab_ll,kk},4,MRSCont.flags.isSERIES);
raw = io_loadspec_sdat(MRSCont.files{metab_ll,kk},4,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw.flags.isHERMES = 1;
elseif MRSCont.flags.isHERCULES
raw = io_loadspec_sdat(MRSCont.files{metab_ll,kk},4,MRSCont.flags.isSERIES);
raw = io_loadspec_sdat(MRSCont.files{metab_ll,kk},4,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw.flags.isHERCULES = 1;
end
% Add NIfTI-MRS information
Expand All @@ -91,17 +91,17 @@
if MRSCont.flags.hasMM %re_mm
temp_ll = MRSCont.opts.MultipleSpectra.mm(ll);
if MRSCont.flags.isUnEdited %re_mm
raw_mm = io_loadspec_sdat(MRSCont.files_mm{temp_ll,kk},1,MRSCont.flags.isSERIES); %re_mm
raw_mm = io_loadspec_sdat(MRSCont.files_mm{temp_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle); %re_mm
[raw_mm] = op_rmempty(raw_mm); %re_mm
raw_mm.flags.isUnEdited = 1;
elseif MRSCont.flags.isMEGA %re_mm
raw_mm = io_loadspec_sdat(MRSCont.files_mm{temp_ll,kk},2,MRSCont.flags.isSERIES); %re_mm
raw_mm = io_loadspec_sdat(MRSCont.files_mm{temp_ll,kk},2,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle); %re_mm
raw_mm.flags.isMEGA = 1;
elseif MRSCont.flags.isHERMES%re_mm
raw_mm = io_loadspec_sdat(MRSCont.files_mm{temp_ll,kk},1,MRSCont.flags.isSERIES); %re_mm
raw_mm = io_loadspec_sdat(MRSCont.files_mm{temp_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle); %re_mm
raw_mm.flags.isHERMES = 1;
elseif MRSCont.flags.isHERCULES %re_mm
raw_mm = io_loadspec_sdat(MRSCont.files_mm{temp_ll,kk},1,MRSCont.flags.isSERIES); %re_mm
raw_mm = io_loadspec_sdat(MRSCont.files_mm{temp_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle); %re_mm
raw_mm.flags.isHERCULES = 1;
end
% Add NIfTI-MRS information
Expand All @@ -113,23 +113,23 @@
if MRSCont.flags.hasRef
ref_ll = MRSCont.opts.MultipleSpectra.ref(ll);
if MRSCont.flags.isUnEdited
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},1,MRSCont.flags.isSERIES);
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw_ref = op_combine_water_subspecs(raw_ref,0);
raw_ref.flags.isUnEdited = 1;
elseif MRSCont.flags.isMEGA
try % GO 03042024: this works for the JHU patch only but throws an error for product MEGA
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},2,MRSCont.flags.isSERIES);
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},2,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
catch % GO 03042024: this works for product MEGA
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},1,MRSCont.flags.isSERIES);
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
end
raw_ref = op_combine_water_subspecs(raw_ref,0);
raw_ref.flags.isMEGA = 1;
elseif MRSCont.flags.isHERMES
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},1,MRSCont.flags.isSERIES);
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw_ref = op_combine_water_subspecs(raw_ref,0);
raw_ref.flags.isHERMES = 1;
elseif MRSCont.flags.isHERCULES
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},1,MRSCont.flags.isSERIES);
raw_ref = io_loadspec_sdat(MRSCont.files_ref{ref_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw_ref = op_combine_water_subspecs(raw_ref,0);
raw_ref.flags.isHERCULES = 1;
end
Expand All @@ -139,7 +139,7 @@
end
if MRSCont.flags.hasWater
w_ll = MRSCont.opts.MultipleSpectra.w(ll);
raw_w = io_loadspec_sdat(MRSCont.files_w{w_ll,kk},1,MRSCont.flags.isSERIES);
raw_w = io_loadspec_sdat(MRSCont.files_w{w_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw_w = op_combine_water_subspecs(raw_w,0);
raw_w.flags.isUnEdited = 1;
% Add NIfTI-MRS information
Expand All @@ -151,19 +151,19 @@
if MRSCont.flags.hasMMRef
temp_ll = MRSCont.opts.MultipleSpectra.mm_ref(ll);
if MRSCont.flags.isUnEdited
raw_mm_ref = io_loadspec_sdat(MRSCont.files_mm_ref{temp_ll,kk},1,MRSCont.flags.isSERIES);
raw_mm_ref = io_loadspec_sdat(MRSCont.files_mm_ref{temp_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw_mm_ref = op_combine_water_subspecs(raw_mm_ref,0);
raw_mm_ref.flags.isUnEdited = 1;
elseif MRSCont.flags.isMEGA
raw_mm_ref = io_loadspec_sdat(MRSCont.files_mm_ref{temp_ll,kk},2,MRSCont.flags.isSERIES);
raw_mm_ref = io_loadspec_sdat(MRSCont.files_mm_ref{temp_ll,kk},2,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw_mm_ref = op_combine_water_subspecs(raw_mm_ref,0);
raw_mm_ref.flags.isMEGA = 1;
elseif MRSCont.flags.isHERMES
raw_mm_ref = io_loadspec_sdat(MRSCont.files_mm_ref{temp_ll,kk},1,MRSCont.flags.isSERIES);
raw_mm_ref = io_loadspec_sdat(MRSCont.files_mm_ref{temp_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw_mm_ref = op_combine_water_subspecs(raw_mm_ref,0);
raw_mm_ref.flags.isHERMES = 1;
elseif MRSCont.flags.isHERCULES
raw_mm_ref = io_loadspec_sdat(MRSCont.files_mm_ref{temp_ll,kk},1,MRSCont.flags.isSERIES);
raw_mm_ref = io_loadspec_sdat(MRSCont.files_mm_ref{temp_ll,kk},1,MRSCont.flags.isSERIES,MRSCont.opts.load.undoPhaseCycle);
raw_mm_ref = op_combine_water_subspecs(raw_mm_ref,0);
raw_mm_ref.flags.isHERCULES = 1;
end
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3 changes: 2 additions & 1 deletion process/OspreyProcess.m
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Expand Up @@ -391,7 +391,8 @@
% actually have negative polarity, but end up positive in the data, so
% that the spectrum needs to be flipped.
if ~isfield(MRSCont.opts.SubSpecAlignment, 'polResidCr')
if isfield(MRSCont.opts.SubSpecAlignment, 'PreservePolarity') && ~MRSCont.opts.SubSpecAlignment.PreservePolarity
if ~isfield(MRSCont.opts.SubSpecAlignment, 'PreservePolarity') || ...
(isfield(MRSCont.opts.SubSpecAlignment, 'PreservePolarity') && ~MRSCont.opts.SubSpecAlignment.PreservePolarity)
raw_Cr = op_freqrange(raw,2.8,3.2);
% Determine the polarity of the respective peak: if the absolute of the
% maximum minus the absolute of the minimum is positive, the polarity
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