Problem converting and displaying Dicom(ultrasonics) image for Matrix

I have a project to read a DICOM file and determine if it is a DICOM file or not. Then read the content of the file and convert it to Matrix and then display it as an image. But unfortunately the picture always appears like this for me

But when I view the image in another program, it appears in its true form

      
            
    elseif strcmp(Group,'7FE0')
        
        if strcmp(Element,'0010')
            
                if dicom_data{7,5}==16
                   
                   dcmImage = uint16(fread(fID,[dicom_data{5,5} dicom_data{6,5}],'uint16')');
                   dicom_data{10,5} = dcmImage;
                else
                   dcmImage = uint16(fread(fID,[dicom_data{5,5} dicom_data{6,5}],'uint8')');
                   dicom_data{10,5} = dcmImage;   
                end
            else
                fseek(fID,ValueLength,0);
        end
    else
      
         if(ftell(fID)==DateiEnde)
            break      
        end
        fseek(fID,ValueLength,0);
        end 
        end
imshow(dicom_data,[0 2^dicom_data{9,5}])

This is the data it reads from the DICOM file

ans =

  10×5 cell array

    {'TransferSyntax' }    {'2'   }    {'10' }    {'UI'}    {'1.2.840.10008.1…'}
    {'PatientName'    }    {'10'  }    {'10' }    {'PN'}    {'no patient'       }
    {'SamplesPerPixel'}    {'28'  }    {'2'  }    {'US'}    {[                3]}
    {'NumberOfFrames' }    {'28'  }    {'8'  }    {'IS'}    {  2×1   char       }
    {'Rows'           }    {'28'  }    {'10' }    {'US'}    {[              512]}
    {'Cols'           }    {'28'  }    {'11' }    {'US'}    {[              512]}
    {'BitsAllocated'  }    {'28'  }    {'100'}    {'US'}    {[                8]}
    {'BitsStored'     }    {'28'  }    {'101'}    {'US'}    {[                8]}
    {'HighBit'        }    {'28'  }    {'102'}    {'US'}    {[                7]}
    {'PixelData'      }    {'7FE0'}    {'10' }    {'OB'}    {512×512 uint16     }

[Walter Roberson]

                   dcmImage = uint16(fread(fID,[dicom_data{5,5} dicom_data{6,5}],'uint16')');

Is the data stored Big Endian or Little Endian?

[Khaled Al Hamidi]

@Walter Roberson Big Endian

[Walter Roberson]

The default for fread is "native", and on all systems currently supported, that is Little Endian. In order to get Big Endian you need to specify it at the time you fopen() or the time you fread()

[Khaled Al Hamidi]

@Walter Roberson i tried it with add 'b' but nothing has changed

[Walter Roberson]

As an experiment, try

imshow(swapbytes(dcmImage))

[Khaled Al Hamidi]

@Walter Roberson

Thank you

I found the problem related to the size of the array, I changed it to another size and the problem was solved

from:

dcmImage = uint8(fread(fID,[dicom_data{5,5} dicom_data{6,5}],'uint8')');   

to:

dcmImage = uint8(fread(fID,[1536 512],'uint8')');

but I got a non-rectangular image

[Walter Roberson]

Experiment with reversing the size numbers in the fread()

Answer 1

[aditi bagora]

Hello Khaled,

I understand you want to read a DICOM (ultrasonics) file and extract the values from its metadata. It seems that you are currently using the "fread()" and "fseek()" functions to read the binary file. However, you are encountering issues when reading the pixel data, which could be due to a mismatch in reading the binary data in a particular format or inconsistent data in the file.

To overcome these issues, you can manually try reading the binary file using "fread()" and "fseek()", you can try using the "dicomread()" and "dicominfo()" functions. These functions are specifically designed to read pixel data and metadata from DICOM files, ensuring compatibility and accurate extraction.

To read the pixel data and dicom data, you can refer to the following example code:

pixel_data = dicomread(filename); % read pixel data

imshow(pixel_data);

dicom_data = dicominfo(filename); % To read the DICOM metadata.

Please refer to the following links for more information:

• Read metadata from DICOM message - MATLAB dicominfo - MathWorks India
• Read DICOM image - MATLAB dicomread - MathWorks India
• Accessing data in DICOM files - MATLAB & Simulink (mathworks.com)
• How to check if file is a dicom file or not

Hope this helps!

Regards,

Aditi

[Walter Roberson]

The purpose of the project was to learn how to use low-level facilities to work with files.