Problem with sprintf and read DICOM images

Dear all,

I have CT slices and I would like to load (imread) them to the Workspace. But I always read only one (first) slice (image). This is my code:

for p=1:38

         filename = sprintf('C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/000048.dcm',p);

          X(:,:,1,p) = dicomread(filename);

I don´t know, where mistake is.

Can you advise me? Thank you for your answers.

Answer 1

[Jan]

There is no format specifier in the format string of sprintf:

sprintf('C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/000048.dcm',p);

This is the same string for all iterations. Perhaps you want:

filename = sprintf('C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/%06d.dcm', p);

[Veronika]

Okay, it will help, but my first CT scan is 000048.dcm not 000001.dcm. Could I somehow ensure this?

Error using dicomread>getFileDetails (line 1458)
File "C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/000001.dcm" not found.

[Jan]

@Veronika: :-) Then start the loop at 48:

Folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';  % Nicer
for p = 48:86
  filename = fullfile(Folder, sprintf('%06d.dcm', p));
  X(:, : , 1, p - 47) = dicomread(filename);
end

Or:

for p = 1:38
  filename = fullfile(Folder, sprintf('%06d.dcm', p + 47));
  X(:, : , 1, p) = dicomread(filename)
end

[Veronika]

Thank you.:-)

[Jan]

You are welcome.

[mohd akmal masud]

HI.. May i know what is the meaning for "p = 48:86" and "for p = 1:38" actually?

if i have 135 slice CT images, what should i writ the value of p?

[Walter Roberson]

first_to_read = 48;
last_to_read = 86;
num_to_read = last_to_read - first_to_read + 1;

Now you can use

for file_idx = 1 : num_to_read
  img_number = file_idx + first_to_read - 1;
  filename = fullfile(Folder, sprintf('%06d.dcm', img_number));
  X(:, : , 1, file_idx) = dicomread(filename);
end

in which case file_idx refers to the relative number to read, which can be quite useful for several different reasons.

You could also use

for file_number = first_to_read : last_to_read
  file_idx = file_number - first_to_read + 1;
  filename = fullfile(Folder, sprintf('%06d.dcm', img_number));
  X(:, : , 1, file_idx) = dicomread(filename);
end

which is sometimes easier to read. But in practice it turns out to be easier to work with relative indices in a for loop: when relative indices are used it is not necessary that the values be consecutive:

files_to_read = [48:63 72:78 85];   %does not need to be consecutive
num_to_read = length(files_to_read);
for file_idx = 1 : num_to_read
  img_number = files_to_read(file_idx);
  filename = fullfile(Folder, sprintf('%06d.dcm', img_number));
  X(:, : , 1, file_idx) = dicomread(filename);
end

[mohd akmal masud]

Dear Walter Roberson,

I used this command to read multiple image CT. i have 135 slice CT images (in format dicom). My first image name start with "CTAC001_CT001.dcm" until "CTAC001_CT135.dcm"

I used this command:

for file_number = first_to_read : last_to_read
  file_idx = file_number - first_to_read + 1;
  filename = fullfile(Folder, sprintf('%06d.dcm', img_number));
  X(:, : , 1, file_idx) = dicomread(filename);
end

Undefined function or variable 'first_to_read'.

But the ERROR appear as below:

Error in trymultipleimages (line 1)
for file_number = first_to_read : last_to_read

Can you help me please...

[Walter Roberson]

Notice my lines near the beginning,

first_to_read = 48;
last_to_read = 86;

[mohd akmal masud]

Meaning that, i have to write like this:

first_to_read = CTAC001_CT001.dcm;
last_to_read = CTAC001_CT135.dcm;
num_to_read = last_to_read - first_to_read + 1;

for file_number = first_to_read : last_to_read
  file_idx = file_number - first_to_read + 1;
  filename = fullfile(Folder, sprintf('%06d.dcm', img_number));
  X(:, : , 1, file_idx) = dicomread(filename);
end

is it correct?

[Walter Roberson]

last_to_read = 135;
for file_number = 1 : last_to_read
  filename = fullfile(Folder, sprintf('CTAC001_CT%03d.dcm', file_number));
  X(:, : , 1, file_number) = dicomread(filename);
  if file_number == 1 && last_to_read ~= 1
    X(end, end, end, last_to_read) = 0;
  end
end

The special test for file_number 1 is a performance optimization to avoid having to grow the array every iteration.

[mohd akmal masud]

Dear Walter Roberson,

The code is successfully. I have try for 135 slices CT images and also 135 slices PET images.

But how come to me to show it in figure (i mean use command imshow)

[Walter Roberson]

It cannot be shown in a single figure using imshow. imshow() is not suitable for volume visualization.

If you have R2017a or newer, try

volumeViewer( permute(X, [1 2 4 3]) )