In one of my GUIs I load DICOM images. Sometimes they are just a volume and another dimension and when I load them in Matlab everything ends up where I want it.
handles.inf = dicominfo([filepath filename]);
handles.dat = dicomread(handles.inf);
size(handles.dat)
ans = 128 128 128 512
For an 128 by 128 by 128 volume at 512 timepoints for example (actually the third dimension would not even be 128, the third dimension is stacks, of which I don't know what it is). However sometimes There are more dimensions in the dicom, but the reader just puts all of them in the fourth dimension.
handles.inf = dicominfo([filepath filename]);
handles.dat = dicomread(handles.inf);
size(handles.dat)
ans = 128 128 1 4082
For a single 128 by 128 slice with 512 timepoints, two echoes and magnitude, phase, real and imaginary data for example.
It is then very hard to unscramble them. Manually I can do this for every DICOM I load but when in a GUI I would want to have a general approach that just creates a dimension in the array for each dimension in the dicom.
This is especially important not just for data-analysis, but also to transform the coordinates from image space to patient space. My own approach was to look at the header, but there's no guarantee that certain entries will work, and the order in which they are applied I can't find. The header entries I found so far:
inf.Rows;%inf.width;%inf.MRAcquisitionFrequencyEncodingSteps;%inf.MRAcquisitionPhaseEncodingStepsInPlane
inf.Columns;% inf.height; % inf.NumberOfKSpaceTrajectories;
inf.MRSeriesNrOfSlices
inf.MRSeriesNrOfEchoes
inf.MRSeriesNrOfDynamicScans
inf.MRSeriesNrOfPhases
inf.MRSeriesReconstructionNumber % not sure about this one
inf.MRSeriesNrOfDiffBValues
inf.MRSeriesNrOfDiffGradOrients
inf.MRSeriesNrOfLabelTypes
reshapeddat = reshape(dat, [all dimension sizes from header here]);
I'm not sure how to check if I've got all variables and what the right order for the reshape. Anybody knows of a sure-fire way to get all dimension sizes from the DICOM header and the order in which they are stacked?
Ok so I now manually go by all possible dimensions. When a stack also contains reconstructed data which has less dimensions than the rest, remove those first.
This is how I check the dimensions:
info = dicominfo(filename);
datorig = dicomread(filename);
%dimension sizes per frame
nrX = double(info.Rows); %similar nX;% info.width;% info.MRAcquisitionFrequencyEncodingSteps;% info.MRAcquisitionPhaseEncodingStepsInPlane
nrY = double(info.Columns); %similar nY;% info.height;% info.NumberOfKSpaceTrajectories;
%dimensions between frames
nrEcho = double(info.MRSeriesNrOfEchoes);
nrDyn = double(info.MRSeriesNrOfDynamicScans);
nrPhase = double(info.MRSeriesNrOfPhases);
nrSlice = double(info.MRSeriesNrOfSlices); %no per frame struct entry, calculate from offset.
%nr of frames
nrFrame = double(info.NumberOfFrames);
nrSeq = 1; % nSeq not sure how to interpret this, wheres the per frame struct entry?
nrBval = double(info.MRSeriesNrOfDiffBValues); % nB
nrGrad = double(info.MRSeriesNrOfDiffGradOrients); % info.MRSeriesNrOfPhaseContrastDirctns;%similar nGrad?
nrASL = 1; % info.MRSeriesNrOfLabelTypes;%per frame struct entry?
imtype = cell(1, nrFrame);
for ii = 1:nrFrame
%imtype(ii) = eval(sprintf('info.PerFrameFunctionalGroupsSequence.Item_%d.PrivatePerFrameSq.Item_1.MRImageTypeMR', ii));
imtype{ii} = num2str(eval(sprintf('info.PerFrameFunctionalGroupsSequence.Item_%d.PrivatePerFrameSq.Item_1.MRImageTypeMR', ii)));
end
imType = unique(imtype, 'stable');
nrType = length(imType);
This is how I reformat the dimensions:
%% count length of same dimension positions from start
if nrEcho > 1
for ii = 1:nrFrame
imecno(ii) = eval(sprintf('inf.PerFrameFunctionalGroupsSequence.Item_%d.PrivatePerFrameSq.Item_1.EchoNumber', ii));
end
lenEcho = find(imecno ~= imecno(1), 1, 'first') - 1;
else
lenEcho = nrFrame;
end
if nrDyn > 1
for ii = 1:nrFrame
imdynno(ii) = eval(sprintf('inf.PerFrameFunctionalGroupsSequence.Item_%d.PrivatePerFrameSq.Item_1.TemporalPositionIdentifier', ii));
end
lenDyn = find(imdynno ~= imdynno(1), 1, 'first') - 1;
else
lenDyn = nrFrame;
end
if nrPhase > 1
for ii = 1:nrFrame
imphno(ii) = eval(sprintf('inf.PerFrameFunctionalGroupsSequence.Item_%d.PrivatePerFrameSq.Item_1.MRImagePhaseNumber', ii));
end
lenPhase = find(imphno~=imphno(1), 1, 'first') - 1;
else
lenPhase = nrFrame;
end
if nrType > 1
q = 1;
imtyno(1, 1) = q;
for ii = 2:nrFrame
if imtype{:, ii-1} ~= imtype{:, (ii)}
q = q+1;
end
imtyno(1, ii) = q;
%for jj = 1:nrType
%if imtype{:,ii} == imType{:,jj}
% imtyno(1, ii) = jj;
%end
%end
end
if q ~= nrType
nrType = q;
end
lenType = find(imtyno ~= imtyno(1), 1, 'first') - 1;
else
lenType = nrFrame;
end
% slices are not numbered per frame, so get this indirectly from location
% currently not sure if working for all angulations
for ii = 1:nrFrame
imslice(:,ii) = -eval(['inf.PerFrameFunctionalGroupsSequence.Item_',sprintf('%d', ii),'.PlanePositionSequence.Item_1.ImagePositionPatient']);
end
% stdsl = std(imslice,[],2); --> Assumption
% dirsl = max(find(stdsl == max(stdsl)));
imslices = unique(imslice', 'rows')';
if nrSlice > 1
for ii = 1:nrFrame
for jj = 1:nrSlice
if imslice(:,ii) == imslices(:,nrSlice - (jj-1)); %dirsl or :?
imslno(1, ii) = jj;
end
end
end
lenSlice = find(imslno~=imslno(1), 1, 'first')-1;
else
lenSlice = nrFrame;
end
if nrBval > 1
for ii = 1:nrFrame
imbno(ii) = eval(sprintf('inf.PerFrameFunctionalGroupsSequence.Item_%d.PrivatePerFrameSq.Item_1.MRImageDiffBValueNumber', ii));
end
lenBval = find(imbno~=imbno(1), 1, 'first') - 1;
else
lenBval = nrFrame;
end
if nrGrad > 1
for ii = 1:nrFrame
imgradno(ii) = eval(sprintf('inf.PerFrameFunctionalGroupsSequence.Item_%d.PrivatePerFrameSq.Item_1.MRImageGradientOrientationNumber', ii));
end
lenGrad = find(imgradno~=imgradno(1), 1, 'first')-1;
else
lenGrad = inf.NumberOfFrames;
end
lenSeq = nrFrame; % dont know how to get this information per frame, in my case always one
lenASL = nrFrame; % dont know how to get this information per frame, in my case always one
%this would have been the goal format
goaldim = [nrSlice nrEcho nrDyn nrPhase nrType nrSeq nrBval nrGrad nrASL]; % what we want
goallen = [lenSlice lenEcho lenDyn lenPhase lenType lenSeq lenBval lenGrad lenASL]; % what they are
[~, permIX] = sort(goallen);
dicomdim = zeros(1, 9);
for ii = 1:9
dicomdim(1, ii) = goaldim(permIX(ii));
end
dicomdim = [nrX nrY dicomdim];
%for any possible zero dimensions from header use a 1 instead
dicomdim(find(dicomdim == 0)) = 1;
newdat = reshape(dat, dicomdim);
newdim = size(newdat);
newnonzero = length(newdim(3:end));
goalnonzero = permIX(1:newnonzero);
[dummyy, goalIX] = sort(goalnonzero);
goalIX = [1 2 goalIX+2];
newdat = permute(newdat, goalIX);
newdat = reshape(newdat, [nrX nrY goaldim]);
When Ive used this as a function for a longer period and debugged it a bit I might post in on the file exchange of mathworks.
来源：https://stackoverflow.com/questions/21755906/dicom-dimensions-in-matlab-array-all-frames-end-up-in-last-dimension-of-array