How to resize multiple dicom images in subfolders and save them?

I have multiple subfolders with many MR dicom images with different size. How can I resize them into 128x128 and save them in the same subfolders at once? Thank you in advance!

Answer 1

[yanqi liu]

fd = fullfile(pwd, 'dcms');
fs = ls(fullfile(fd, '*.dcm'));
for i = 1 : size(fs,1)
    im = dicomread(fullfile(fd, strtrim(fs(i,:))));
    im = imresize(im, [128 128], 'bilinear');
    imwrite(im, fullfile(fd, [strtrim(fs(i,:))) '_128x128.dcm']));
end

[Shourya]

@yanqi liu Thank you for your response. I tried the code and I am getting the following error.

Error in dicomread>newDicomread (line 194)

fileDetails = images.internal.dicom.getFileDetails(filename, verifyIsDICOM);

Error in dicomread (line 91)

[X, map, alpha, overlays] = newDicomread(msgname, frames, useVRHeuristic);

Error in resize (line 4)

im = dicomread(fullfile(fd, strtrim(fs(i,:))));

[Rik]

That error message is not quite complete.

Did you verify your files are valid DICOM files that Matlab can read?

[Shourya]

@Rik Thank you for your response. They are in .dcm format and it says unable to load the file_name.dcm and throws that error. I dont understand why.

But I did resize them using these lines and it worked. I am not sure if its right.

folder = 'E:/Project/Dataset/Images_1';

filelist = dir(fullfile(folder,'*.dcm'));

total_images = numel(filelist);

op_folder = 'E:/Project/Dataset/op_images';

for n = 1:total_images

f = fullfile(folder, filelist(n).name);

my_images = dicomread(f);

resize = imresize(my_images, [128 128]);

output = fullfile(op_folder, filelist(n).name);

dicomwrite(resize, output);

end

[yanqi liu]

yes，sir，can you upload one file to debug

[Shourya]

@yanqi liu thank you for your response. I tried uploading but website says file format not supported. I have changed it to .mat not sure if it helps. Thank you.

[Shourya]

Hi I tried the above code on multiple folders with dcm images and I am getting the following error. Can someone please help me?

(Posted the code I am refering to)

folder = 'E:/Project/Dataset';

filelist = dir(fullfile(folder,'**/*.dcm'));

total_images = numel(filelist);

op_folder = 'E:/Project/Dataset/op_images';

for n = 1:total_images

f = fullfile(folder, filelist(n).name);

my_images = dicomread(f);

resize = imresize(my_images, [128 128]);

output = fullfile(op_folder, filelist(n).name);

dicomwrite(resize, output);

end

--------------------------------------

Error:

Dot indexing is not supported for variables of this type.

Error in Prog_2 (line 7)

f = fullfile(folder, filelist(n).name);

[yanqi liu]

yes，sir，may be use

f = fullfile(filelist(n).folder, filelist(n).name);

to replace line 7

[Shourya]

Hello @yanqi liu. Thank you for your response. The code works, but it stops at a certain point and displays the warning below.

Warning: Not enough data imported. Attempted to read 117886 bytes at position 2138. Only read 13222. > In dicomread>newDicomread (line 204)

I was unable to resize all images. Sorry for the trouble, but I'm not sure what went wrong.

[Shourya]

Can someone please help me with this warning and problem. As mentioned above I am not able to resize and save all the images. I get the following warning and the code terminates.

Warning: Not enough data imported. Attempted to read 117886 bytes at position 2138. Only read 13222. > In dicomread>newDicomread (line 204)

[Rik]

Your error seems due to your dicom file, so not something we can debug for you remotely. Unless you use a custom dicom reader and haven't told us yet.

[Shourya]

@Rik Thank you for your response. I am not using any dicom reader. I am not sure what is the issue. I just have MR images saved in .dcm format. They are just image files without any metadata. I don't know how to confirm if the images are readable, there are thousands of images with many folders.