Am I writing an image volume correctly from the Dicom files in a directory?

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Hello everyone, I want to make sure whether the below scripts are good to write a image 3D volume using the DICOM images located in a linux directory:
% List all files in the directory
filePattern = dir('/etc/Dicom_files/');
% Remove . and .. directories
im_files = filePattern;
im_files = im_files(~ismember({im_files.name}, {'.','..'}));
% For all slice locations
slLoc = zeros(numel(im_files),1);
% Pre-allocate mage volume -manually read the image slice and use that info
imVol = zeros(256, 256, 71);
dictionaryIn = "dicom-dict.txt";
dicomdict("set",dictionaryIn);
for k = 1 : numel(im_files)
baseFileName = im_files(k).name;
fullFileName = fullfile(im_files(k).folder, baseFileName);
%fprintf(1, 'Now reading %s\n', fullFileName);
imVol(:, :, k) = dicomread(fullFileName);
% Visualize 3D volume
Volume = imshow(imVol(:,:,k)); colormap gray;
% Read DICOM header
hdr = dicominfo(fullFileName, "dictionary", dictionaryIn);
% Pull slice locations from all slices as a column vector
if isfield(hdr, 'SliceLocation')
slLoc(k,1) = hdr.SliceLocation;
end
end
imVol = single(imVol);
slLoc = single(sort(slLoc));
Thank you for your help in advance.

Answers (1)

Simon Chan
Simon Chan on 7 Jul 2022
Looks good except the last two lines.
You know the slice location may not be in a correct order and you sort it in the last line. However, the image set is not sorted in the same order and hence there exist inconsistency between the slice location and image set imVol.
Just simply output the index when using function sort and use it to sort the image set as shown in the last line below:
for k = 1 : numel(im_files)
baseFileName = im_files(k).name;
fullFileName = fullfile(im_files(k).folder, baseFileName);
%fprintf(1, 'Now reading %s\n', fullFileName);
imVol(:, :, k) = dicomread(fullFileName);
% Visualize 3D volume
Volume = imshow(imVol(:,:,k),[]); % <-- Also Change here, but it's up to you
%colormap gray; % Remove this line
% Read DICOM header
hdr = dicominfo(fullFileName, "dictionary", dictionaryIn);
% Pull slice locations from all slices as a column vector
if isfield(hdr, 'SliceLocation')
slLoc(k,1) = hdr.SliceLocation;
end
end
[slLoc,index] = sort(slLoc); % Sort the slice location and keep the index
slLoc = single(slLoc);
imVol = single(imVol(:,:,index)); % Rearrange the images so that it matches the slice Location
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