First input must be a file name or a file identifier.

I get the error at line

[Img] = DicomReader(theFiles)

and

dicom_header = dicominfo(filename);

The code:

N=15;

img_dir = 'D:\stelios phd files\DesMoines\karadokei\'

filePattern = fullfile(img_dir, '*.dcm');
theFiles = dir(filePattern);
for k= 1:length(theFiles)
    baseFileName = theFiles(k).name;
    fullFileName = fullfile(img_dir, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);

   % Now do whatever you want with this file name,
   % such as reading it in as an image array with imread()
    imageArray = dicomread(baseFileName);

end

D = squeeze(imageArray)

[Img] = DicomReader(D,N)

[KSSV]

It seems DicomReader wants a file name.....but you are inputting some numbers into it.

[Guillaume]

I get the error at DicomReader ...

With us not knowing what your DicomReader function does, how can we tell you what the problem is? The error is clear whatever function you're using wants a file name or a file identifier and that is not what you are giving it.

[Stelios Fanourakis]

function Img = DicomReader(filename,N)
dicom_header = dicominfo(filename);
file_names = dir([filename(1) '*']);
Img = zeros([dicom_header.Width, dicom_header.Height, length(file_names)]);
minSliceNo = Inf;
maxSliceNo = 0;
 for i = 1:N
     dicom_header = dicominfo(file_names(i).name);
 if dicom_header.InstanceNumber < minSliceNo
 minSliceNo = dicom_header.InstanceNumber;
end
if dicom_header.InstanceNumber > maxSliceNo
maxSliceNo = dicom_header.InstanceNumber;
end
Img(:,:,dicom_header.InstanceNumber) = dicomread(dicom_header);
end
Img = Img(:,:,minSliceNo:maxSliceNo);
end

[Stelios Fanourakis]

But now I have another problem. Can someone who knows dicom very well please explain me the Instance Number and Acquisition Numbers tags what do they mean and what values can we insert if they are not predefined?

Answer 1

[Ameer Hamza]

dir() only return file names, not complete paths. You need to specify the full path to dicomread(), Change the line like this

 imageArray = dicomread(fullFileName);

[Stelios Fanourakis]

Unfortunately it wasn't that fault Ameer

Answer 2

[Guillaume]

function Img = DicomReader(filename,N)

Clearly your function expects a filename as the first argument

D = squeeze(imageArray)
[Img] = DicomReader(D,N)

Yet, you give it an imagearray. I don't understand why you expected that to work.

In addition, you're creating the imageArray in the loop but at each iteration you're overwriting the previous imageArray. So after the loop, imageArray is just the last image and you've discarded all the other ones.

[Stelios Fanourakis]

I corrected everything you suggested but still comes the same error.

imageArray = dicomread(fullFileName);

filename = squeeze(imageArray)

[Img] = DicomReader(filename,N)

imageArray is out of for loop

[Guillaume]

The name of the variable is irrelevant. No matter what you call it you are still passing an image to DicomReader, not a filename.

I have no idea what you're trying to do but your code makes no sense. You read images in a loop to immediately discard the images without doing anything with them. After the loop, you're left with the last image only, which you pass to another function which expects a filename not an image.