i wanted to read .dcm files for my project from a folder
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can anyone give me code to read the dicom files from folder and
X = repmat(int16(0), [128 128 1 200]);
dicomFiles = dir('E:\SHIVA BACKUP\THYROID\P1\newcodes\data1\13002\*.dcm');
y=length(dicomFiles)
% Read the series of images.
for p=1:y
%filename = sprintf('IM_%01d.dcm', p);
X(:,:,1,p) = dicomread(dicomFiles);
end
% Display the image stack.
montage(X,[])
Risposta accettata
Walter Roberson
il 14 Nov 2016
projectdir = 'E:\SHIVA BACKUP\THYROID\P1\newcodes\data1\13002';
dicomFiles = dir( fullfile(projectdir, '*.dcm' ));
y = length(dicomFiles)
X = zeros(128, 128, 1, y, 'uint8');
% Read the series of images.
for p=1:y
filename = fullfile( projectdir, dicomFiles(p).name );
X(:,:,1,p) = dicomread(filename);
end
% Display the image stack.
montage(X,[])
14 Commenti
andhavarapu lokesh
il 14 Nov 2016
Walter Roberson
il 14 Nov 2016
The below will probably emit some messages, but we will need to know the sizes that it reports.
projectdir = 'E:\SHIVA BACKUP\THYROID\P1\newcodes\data1\13002';
dicomFiles = dir( fullfile(projectdir, '*.dcm' ));
y = length(dicomFiles)
X = zeros(128, 128, 1, y, 'uint8');
% Read the series of images.
for p=1:y
filename = fullfile( projectdir, dicomFiles(p).name );
imdata = dicomread(filename);
imsize = size(imdata);
if ~isequal( imsize, [128 128] )
fprintf('file is unexpected size %s instead of [128 128], skipping "%s"\n', mat2str(imsize), filename);
else
X(:,:,1,p) = imdata;
end
% Display the image stack.
montage(X,[])
andhavarapu lokesh
il 14 Nov 2016
Modificato: Walter Roberson
il 14 Nov 2016
andhavarapu lokesh
il 14 Nov 2016
Walter Roberson
il 14 Nov 2016
You have a problem. Each of the .dcm files has 72 slices stored in it. You can represent any one of them in 3D, but you would need to add another dimension to represent the series of 200 of them, such as if you were to use animation for them.
projectdir = 'E:\SHIVA BACKUP\THYROID\P1\newcodes\data1\13002';
y = 200;
X = zeros(128, 128, 1, 72, y, 'uint8');
% Read the series of images.
for p=1:y
thisfile = sprintf('%d.dcm', p);
filename = fullfile( projectdir, thisfile );
imdata = dicomread(filename);
imsize = size(imdata);
if ~isequal( imsize, [128 128 1 72] )
fprintf('file is unexpected size %s instead of [128 128 1 72], skipping "%s"\n', mat2str(imsize), filename);
else
X(:, :, :, :, p) = imdata;
end
figure();
% Display the first image stack.
montage(X(:,:,:,:,1), [])
axis image
title('First file, all layers')
figure();
% Display the first layer of all of the stacks
montage( permute( X(:, :, :, 1, :), [1 2 3 5 4]) )
title('First layer of all files')
andhavarapu lokesh
il 14 Nov 2016
andhavarapu lokesh
il 14 Nov 2016
Walter Roberson
il 14 Nov 2016
projectdir = 'E:\SHIVA BACKUP\THYROID\P1\newcodes\data1\13002';
dicomFiles = dir( fullfile(projectdir, '*.dcm' ));
y = length(dicomFiles);
fnums = zeros(1,y);
for p = 1 : y
[~, basename, ~] = fileparts(dicomFiles(p).name);
fnums(p) = str2num(basename);
end
fnums = unique(fnums);
y = length(fnums);
X = zeros(128, 128, 1, 72, y, 'uint8');
% Read the series of images.
for p=1:y
thisfile = sprintf('%d.dcm', fnums(p));
filename = fullfile( projectdir, thisfile );
imdata = dicomread(filename);
imsize = size(imdata);
if ~isequal( imsize, [128 128 1 72] )
fprintf('file is unexpected size %s instead of [128 128 1 72], skipping "%s"\n', mat2str(imsize), filename);
else
X(:, :, :, :, p) = imdata;
end
figure();
% Display the first image stack.
montage(X(:,:,:,:,1), [])
axis image
title('First file, all layers')
figure();
% Display the first layer of all of the stacks
montage( permute( X(:, :, :, 1, :), [1 2 3 5 4]) )
title('First layer of all files')
fprintf('%d files loaded into X, with 72 slices each\n', y);
fprintf('You cannot meaningfully view everything together.\n');
fprintf('I do not know what you hope to be able to do with all of this images, but you have them now.\n');
andhavarapu lokesh
il 14 Nov 2016
Walter Roberson
il 14 Nov 2016
I said
fnums(p) = str2num(basename);
not
fnums(p) = str2num('basename');
andhavarapu lokesh
il 16 Nov 2016
Modificato: Walter Roberson
il 16 Nov 2016
Walter Roberson
il 16 Nov 2016
What message are you getting?
andhavarapu lokesh
il 25 Nov 2016
Walter Roberson
il 25 Nov 2016
I suggest you get vol3d v2 from the file exchange to do the volume rendering on each squeeze(X(:, :, :, :, p))
I do not know anything about calculating volume fraction or isolating ventricles. I always fainted when they did the heart rendering where I worked.
Più risposte (1)
Mostafa Hussien
il 18 Feb 2020
0 voti
i have a folder its name Brain-Tumor-Progressionon Desktop its dicom file how can i read a file insid this folder called PGBM-001 please answer
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