how to read and save dicom images in different directories

I have series of 1600 dicom images with the name 6--12-1.dcm, 6--12-2.dcm, 6--12-3.dcm and so on. how can I read the sequence and do the filtering on images and save them in another folder? here is my code but it gives me errors, can you please help me to correct it:

source_dir=uigetdir([]); %I= dir('C:\Users\Shan\Desktop\CT Images')
pwd
d=dir([source_dir,'\6--12-*.dcm']);
totalfile=length(d); 
resultfolder='C:\Users\Shan\Desktop\CT Images\Median'
for i=1:totalfile
  fname=['6--12-',num2str(i), '.dcm'];
  indicom=dicomread(fname);
  
  subplot(1,2,1), imshow(indicom,[]);
  title('original image number',(num2str(i)),'Interpreter','None')
  
  medianfilter{i}=medfilt2(indicom{i},[4 4]);
  BasedFileName=sprint('%d.dcm',i);
  FilteredFileName=fullfile(resultfolder,BasedFileName)
  dicomwrite(medianfilter, FilteredFileName);
  
  subplot(1,2,2), imshow(medianfilter,[]);
  title('median filtered image number',num2str(i),'Interpreter','None')
end

Answer 1

[Geoff Hayes]

Shel - you are using uigetdir to get the source directory source_dir which you use to query for the number of files in that folder which match the filter

 d=dir([source_dir,'\6--12-*.dcm']);

but you are not using that source_dir when reading the file

 fname=['6--12-',num2str(i), '.dcm'];
 indicom=dicomread(fname);

You will want to include the source directory when reading that file

 indicom=dicomread(fullfile(source_dir, fname));

Try the above and see what happens! If this doesn't help, then please copy and paste the full error message to this question.

[Shel]

well, thank you here is the new code ... please let me know if it is not correct:

source_dir=uigetdir([]); %I= dir('C:\Users\Shan\Desktop\CT Images')
pwd
d=dir([source_dir,'\6--12-*.dcm']);
totalfile=length(d); 
resultfolder='C:\Users\Shan\Desktop\CT Images\Median'
for i=1:totalfile
  fname=['6--12-',num2str(i), '.dcm'];
  indicom=dicomread(fullfile(source_dir, fname));
  
  subplot(1,2,1), imshow(indicom,[]);
  title('original image number',(num2str(i)),'Interpreter','None')
  
  medianfilter{i}=medfilt2(indicom{i},[4 4]);
  BasedFileName=sprint('%d.dcm',i);
  FilteredFileName=fullfile(resultfolder,BasedFileName)
  dicomwrite(medianfilter, FilteredFileName);
  
  subplot(1,2,2), imshow(medianfilter,[]);
  title('median filtered image number',num2str(i),'Interpreter','None')
end

and here is the error:

Error using title (line 21)
Incorrect number of input arguments

Besides, there is no output in

C:\Users\Shan\Desktop\CT Images\Median

[Geoff Hayes]

Please see title for how this function is used. In your case, I suspect you want to combine the title message and number into a string that you then pass as the input to title. Using sprintf you could do

 title(sprintf('median filtered image number %d',i));

As for no files being written to the output folder, please confirm that FilteredFileName is valid. Also, use breakpoints to step through the code to get an idea of what is happening. When the dicomwrite function has been called, check the console (command window) for any errors or warnings.

[Shel]

Hi, thanks for your time. I changed it again several time: here is the code:

source_dir='C:\Users\Shan\Desktop\CT Images';
 d=dir([source_dir,'\6--12-*.dcm']);
 totalfile=length(d); 
 resultfolder='C:\Users\Shan\Desktop\CT Images\Median';
for i=1:totalfile
  fname=['6--12-',num2str(i), '.dcm'];
  %indicom=dicomread(fname);
    indicom=dicomread(fullfile(source_dir, fname));
  subplot(1,2,1), imshow(indicom,[]);
    title(sprintf('original image number %d',i));  
    medianfilter{i}=medfilt2(indicom{i},[4 4]);
BasedFileName=sprint('%d.dcm',i);
  FilteredFileName=fullfile(resultfolder,BasedFileName);
  dicomwrite(medianfilter, FilteredFileName);
  subplot(1,2,2), imshow(medianfilter,[]);
title(sprintf('median filtered image number %d',i));
 end

there is a warning on line 11:

the variable medianfilter appears to change size on every loop iteration (within a script) .consider preallocation for speed

and the error is:

Cell contents reference from a non-cell array object.

[Geoff Hayes]

which line is generating the error? is it this line?

 medianfilter{i}=medfilt2(indicom{i},[4 4]);

why are you treating indicom as if it were a cell array? Wouldn't you just do

 medianfilter{i}=medfilt2(indicom,[4 4]);

instead?

[Shel]

yes that was the line. I corrected the command as you stated there was an error which the function sprint is not defined to I changed

BasedFileName=sprint('%d.dcm',i);

to

BasedFileName=sprintf('%d.dcm',i);

and now it has the error:

Error using dicom_prep_ImagePixel>getPixelStorage (line 204)
Invalid datatype for image pixels.

Error in dicom_prep_ImagePixel (line 13)
[ba, bs, hb, pr] = getPixelStorage(X, txfr, useExistingBitDepths, metadata, dictionary);

Error in dicom_prep_metadata (line 51)
    metadata = dicom_prep_ImagePixel(metadata, X, map, txfr, useMetadataBitDepths, dictionary);

Error in dicom_create_IOD (line 26)
metadata = dicom_prep_metadata(IOD_UID, metadata, X, map, options.txfr,
options.usemetadatabitdepths, dictionary);

Error in dicomwrite>write_message (line 274)
        [attrs, status] = dicom_create_IOD(SOP_UID, X, map, ...

Error in dicomwrite (line 210)
    [status, options] = write_message(X, filename, map, metadata, options);

[Stephen23]

@Shel: read the dicomwrite help, where it clearly lists the accepted data types for the image as "int8 | int16 | uint8 | uint16". Now look at your code: is medianfilter an integer array, as dicomwrite requires, or is it a cell array? (hint: it is a cell array, because that is what you specified it as).

It is not clear why you are putting all of this data into cell arrays as you do not seem to do any processing with them after the loop, so the cell array is probably just a pointless complication. In any case, if you are using cell arrays then you will need to access the data inside the cell array using indexing:

dicomwrite(medianfilter{i},...)