Multiple DICOM files from folder to png conversion

I am trying to convert a folder of 200+ DICOM files (.dcm) to a folder of PNG images and save them, but am stuggling with proper execution of the code (Beginner)

This is what I have so far:

i = 0;
foldername = 'LowerLeg';
outdir = 'lowerleg_imgs';
dicomlist = dir(fullfile(foldername,'*.dcm'));
for cnt = 1 : numel(dicomlist)
    i= i+1;
    thisfile = fullfile(foldername, dicomlist(i).name);
    I{cnt} = dicomread(thisfile);

end
    out_file = [filename, '.', 'png']
    imwrite(I{cnt}, [outdir, out_file])

Answer 1

[Walter Roberson]

foldername = 'LowerLeg';
outdir = 'lowerleg_imgs';

dicomlist = dir(fullfile(foldername,'*.dcm'));
num_files = numel(dicomlist);
I = cell(num_files, 1);
for cnt = 1 : num_files
    thisfile = fullfile(foldername, dicomlist(cnt).name);
    [~, basename] = fileparts(thisfile);
    outfile = fullfile(outdir, basename + ".png");
    I{cnt} = dicomread(thisfile);
    imwrite(I{cnt}, outfile);
end

However, if you do not need all of the data together afterwards, then do not bother to save it:

foldername = 'LowerLeg';
outdir = 'lowerleg_imgs';

dicomlist = dir(fullfile(foldername,'*.dcm'));
num_files = numel(dicomlist);
for cnt = 1 : num_files
    thisfile = fullfile(foldername, dicomlist(cnt).name);
    [~, basename] = fileparts(thisfile);
    outfile = fullfile(outdir, basename + ".png");
    I = dicomread(thisfile);
    imwrite(I, outfile);
end

[Janice Cruz]

Thanks Walter! This code runs without errors but the outdir folder with the png images is still empty. Both the called folders are in the pathway.

foldername = 'Subject2_LowerLeg_Proximal';
outdir = 'Prox_lowerleg_png';
dicomlist = dir(fullfile(foldername,'*.dcm'));
num_files = numel(dicomlist);
I = cell(num_files, 1);
for cnt = 1 : num_files
    thisfile = fullfile(foldername, dicomlist(cnt).name);
    [~, basename] = fileparts(thisfile);
    outfile = fullfile(outdir, basename + ".png");
    I{cnt} = dicomread(thisfile);
    imwrite(I{cnt}, outfile);
end

[Walter Roberson]

Check num_files afterwards. I suspect that it is not locating any dcm files inside the folder.

Answer 2

[yanqi liu]

clc; clear all; close all;
foldername = './LowerLeg';
outdir = './lowerleg_imgs';
if ~exist(outdir, 'dir')
    mkdir(outdir);
end
dicomlist = dir(fullfile(foldername,'*.dcm'));
for cnt = 1 : numel(dicomlist)
    thisfile = fullfile(foldername, dicomlist(cnt).name);
    I{cnt} = dicomread(thisfile);
    out_file = [dicomlist(cnt).name, '.', 'png']
    imwrite(mat2gray(I{cnt}), fullfile(outdir, out_file))
end

[Walter Roberson]

filename is undefined. It obviously needs to be updated each time you read a new file.

I is not being pre-allocated, so it has to grow in place each time you read another image.