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[BUG FIX] - SpectroFrequency nii-mrs header extension issue - io_writeniimrs - Helge #549

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merged 4 commits into from
Jan 12, 2023
Merged

[BUG FIX] - SpectroFrequency nii-mrs header extension issue - io_writeniimrs - Helge #549

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d1786aa
Merge remote-tracking branch 'upstream/develop' into develop
HJZollner Dec 16, 2022
636d129
Merge branch 'develop' of https://github.com/HJZollner/osprey into de…
HJZollner Dec 16, 2022
81fe5f5
Merge branch 'schorschinho:develop' into develop
HJZollner Dec 16, 2022
286836a
[BUG FIX] - SpectroFrequency nii-mrs header extension issue - io_writ…
HJZollner Jan 12, 2023
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39 changes: 19 additions & 20 deletions libraries/FID-A/inputOutput/io_loadspec_niimrs.m
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
%
% USAGE:
% out = io_loadspec_niimrs(filename);
%
%
% DESCRIPTION:
% Reads in MRS data stored according to the NIfTI MRS format.
% See the specification under
% https://docs.google.com/document/d/1tC4ugzGUPLoqHRGrWvOcGCuCh_Dogx_uu0cxKub0EsM/edit
%
% io_loadspec_niimrs outputs the data in structure format, with fields
% corresponding to time scale, fids, frequency scale, spectra, and header
%
% io_loadspec_niimrs outputs the data in structure format, with fields
% corresponding to time scale, fids, frequency scale, spectra, and header
% fields containing information about the acquisition. The resulting matlab
% structure can be operated on by the other functions in this MRS toolbox.
%
Expand All @@ -27,7 +27,7 @@
% This function requires the dcm2nii toolbox (Xiangrui Li) to be on the
% MATLAB path
% https://github.com/xiangruili/dicm2nii
%
%
% INPUTS:
% filename = filename of NIfTI MRS file (*.nii) to load.
%
Expand Down Expand Up @@ -85,7 +85,7 @@
% dim_6 and dim_7.
if isfield(hdr_ext, 'dim_5')
dim_number = 5;

% This field may come in as a cell or a string.
if iscell(hdr_ext.dim_5)
dim_5 = hdr_ext.dim_5{1};
Expand Down Expand Up @@ -120,12 +120,12 @@
otherwise
error('Unknown dimension value specified in dim_5: %s', dim_5);
end

end

if isfield(hdr_ext, 'dim_6')
dim_number = 6;

% This field may come in as a cell or a string.
if iscell(hdr_ext.dim_6)
dim_6 = hdr_ext.dim_6{1};
Expand Down Expand Up @@ -163,7 +163,7 @@
end
if isfield(hdr_ext, 'dim_7')
dim_number = 7;

% This field may come in as a cell or a string.
if iscell(hdr_ext.dim_7)
dim_7 = hdr_ext.dim_7{1};
Expand Down Expand Up @@ -208,7 +208,7 @@

% Find the number of averages. 'averages' will specify the current number
% of averages in the dataset as it is processed, which may be subject to
% change. 'rawAverages' will specify the original number of acquired
% change. 'rawAverages' will specify the original number of acquired
% averages in the dataset, which is unchangeable.
if dims.subSpecs ~= 0
if dims.averages ~= 0
Expand All @@ -229,8 +229,8 @@
end

% FIND THE NUMBER OF SUBSPECS
% 'subspecs' will specify the current number of subspectra in the dataset
% as it is processed, which may be subject to change. 'rawSubspecs' will
% 'subspecs' will specify the current number of subspectra in the dataset
% as it is processed, which may be subject to change. 'rawSubspecs' will
% specify the original number of acquired subspectra in the dataset, which
% is unchangeable.
if dims.subSpecs ~=0
Expand All @@ -253,7 +253,7 @@
dims.y = 0;
dims.z = 0;
fids = squeeze(fids);

%Now that we've indexed the dimensions of the data array, we now need to
%permute it so that the order of the dimensions is standardized: we want
%the order to be as follows:
Expand Down Expand Up @@ -317,13 +317,13 @@
elseif length(sqzDims)==1
dims.t=1;dims.coils=0;dims.averages=0;dims.subSpecs=0;dims.extras=0;
end

%Now get the size of the data array:
sz=size(fids);

%Compared to NIfTI MRS, FID-A needs the conjugate
fids = conj(fids);

%Now take fft of time domain to get fid:
specs=fftshift(fft(fids,[],dims.t),dims.t);

Expand Down Expand Up @@ -387,7 +387,7 @@
out.subspecs = subspecs;
out.rawSubspecs = rawSubspecs;


% Echo/repetition time
out.te = hdr_ext.EchoTime * 1e3; %convert to [ms]
out.tr = hdr_ext.RepetitionTime * 1e3; %convert to [ms]

Expand Down Expand Up @@ -459,7 +459,7 @@
out.flags.isHERCULES = 1;
end

% Store additional information from the nii header
% Store additional information from the nii header
if out.dims.extras
if ischar(out.seq)
temp_seq = out.seq;
Expand All @@ -472,7 +472,7 @@
out.dwelltime(ex) = out.dwelltime(1);
out.centerFreq(ex) = out.centerFreq(1);
out.txfrq(ex) = out.txfrq(1);

if isfield(hdr_ext.(['dim_' num2str(dim_number) '_header']), 'EchoTime')
out.te(ex) = hdr_ext.(['dim_' num2str(dim_number) '_header']).EchoTime(ex) * 1e3; % convert to [ms]
out.extra_names{ex} = ['TE_' num2str(ex)];
Expand All @@ -499,4 +499,3 @@

end
end

4 changes: 4 additions & 0 deletions libraries/FID-A/inputOutput/io_writeniimrs.m
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Original file line number Diff line number Diff line change
Expand Up @@ -159,6 +159,10 @@
in.nii_mrs.hdr_ext.(sprintf('dim_%i',JJ+4)) = dimname{JJ};
end

if ~iscell(in.nii_mrs.hdr_ext.SpectrometerFrequency)
in.nii_mrs.hdr_ext.SpectrometerFrequency = {in.nii_mrs.hdr_ext.SpectrometerFrequency};
end

nii.ext.ecode = 44;
nii.ext.edata_decoded = jsonencode(in.nii_mrs.hdr_ext);
len = int32(numel(nii.ext.edata_decoded));
Expand Down