dicominfo returns an error on all dicom files other than one

Hi all, i have a question. I'm writing some codes to read in the dicom tags of a series of dicom files. but somehow, dicominfo can only read the first data but returns an error on other data.

sourcedata = '/Users/.../dcmonly'
filesandfolders= dir([sourcedata '/**']);
%Plist = setdiff({ P_f([P_f.isdir]).name},{'.','..'});
all_list = {filesandfolders.name};
 
T = cell2table({});
 
for ii = 3: numel(all_list)
    name = all_list{ii}
    info(ii) = dicominfo(name); 
    s2det = [info.DistanceSourceToDetector];
    s2pat = [info.DistanceSourceToPatient];
    
    pixelspace = [info.ImagerPixelSpacing];
    pixelsize = pixelspace * (s2det/s2pat);
    Nf = 1/(2* pixelsize);
    
    % write data to excel 
    T.s2det = s2det;
    T.s2pat = s2pat;
    T.pixelspace = pixelspace(1);
    T.pixelsize = pixelsize(1);
    T.Nf = Nf;
end

this is the error i got

Error using dicom_getFileDetails (line 14)

Unable to load file "00000018.dcm".

Error in dicominfo (line 55)

fileDetails = dicom_getFileDetails(filename);

Error in dicomtags (line 17)

info(ii) = dicominfo(name);

FYI the code after %write data to excel is pretty self explanatory, but i wanna append every info from other dicom files too in the sam excel file. i'm not sure how to go about this either. any help would be very much appreciated!

Answer 1

[Simon Chan]

Below shows some modification based on your code:

(1) Variable all_list is going to contain file names only, so that the index can start from 1 in the for loop

(2) Not indexing the varaible info so that it overwrites every time in the loop. You only needs to put the indexing unless you would like to record all information and process them later.

(3) Verify variable info.DistanceSourceToPatient is not zero in your case. Some vendor does not record this value and just put zero. If this is zero, you cannot calculate the pixel size later in the code

(4) info.PixelSpacing normally has two values, one for x and one for y-dimension. They are the same in most of the case but better to verify it by typing info.PixelSpacing to see both values. The following code take one dimension to calculate the pixelspace only (should be enough).

(5) Result for each dicom image is saved inside the loop and append in the array exceldata

(6) Write data to excel after finishing the loop

sourcedata = '/Users/.../dcmonly';                                      % Your working directory
filesandfolders= dir([sourcedata '/**']);                               % Read all files and folders
all_list = {filesandfolders(~[filesandfolders.isdir]).name};            % Retrieves files only
exceldata = [];                                                         % Initialize an empty array
for ii = 1: numel(all_list)
    name = all_list{ii};                                                % Read the file name
    info = dicominfo(name);                                             % Retrieve the dicom header
    s2det = info.DistanceSourceToDetector;
    s2pat = info.DistanceSourceToPatient;                               
    pixelspace = info.PixelSpacing(1);
    pixelsize = pixelspace * (s2det./s2pat);
    Nf = 1/(2* pixelsize);
    exceldata = [exceldata; s2det s2pat pixelspace pixelsize Nf];       % Append the data
end
writematrix(exceldata,fullfile(sourcedata,'result.xlsx'),'UseExcel',true,'Sheet','Extra','WriteMode','append');

[sesilia maidelin]

thank you!

[sesilia maidelin]

hi simon, i've used this code but it only exports the name of the files to the xlsx file. How do i export the other data?

[Simon Chan]

I accidently write a sheet name 'Extra' in the last line, would you please whether there is any additional sheet called 'Extra' on the excel file?

On the other hand, would you type variable 'result' in the MATLAB Command Window to make sure that it display the data you want?

[sesilia maidelin]

matlab doesn't recognise the variable result, strangely. There was no additional sheet, extra was the sheet the code wrote the data to. But this should be good enough. Thank you simon!

[Simon Chan]

Sorry,typo error

The variable should be 'exceldata', please check againa and sorry about that.

[sesilia maidelin]

yes, but my first column is supposed to be a string. it couldn't write the numbers along with the strings so i just turned the name into number. is there anyway to do that? thank you you've been very helpful!

[Simon Chan]

Now I understand, I was thinking all the data writing to excel are numeric and hence I use writematrix. If there is string in the data, I would use writecell as follows:

The code below also write the file name in the first column as an example.

It includes the headers in the first row of the file as well. You may change the name if you like.

sourcedata = '/Users/.../dcmonly';                                      % Your working directory
filesandfolders= dir([sourcedata '/**']);                               % Read all files and folders
all_list = {filesandfolders(~[filesandfolders.isdir]).name};   
exceldata = {'File name', 's2det', 's2pat', 'pixelspace', 'pixelsize', 'Nf'};                                                         % Initialize an empty cell array
for ii = 1: numel(all_list)
    name = all_list{ii};                                                % Read the file name
    info = dicominfo(name);                                             % Retrieve the dicom header
    s2det = info.DistanceSourceToDetector;
    s2pat = info.DistanceSourceToPatient;                               
    pixelspace = info.PixelSpacing(1);
    pixelsize = pixelspace * (s2det./s2pat);
    Nf = 1/(2* pixelsize);
    data = horzcat({name}, {s2det}, {s2pat}, {pixelspace}, {pixelsize}, {Nf});
    exceldata = vertcat(exceldata, data);      
end
writecell(exceldata,fullfile(sourcedata,'result.xlsx'),'UseExcel',true,'Sheet','Extra','WriteMode','append');

Somthing like this should be found in the excel file, noticed that the data shown below are only for demo purpose, not real data.

[sesilia maidelin]

thank you so much! it works well now :)