Pipeline to access a folder and the subfolders in it until it can retrieve the data

I have a main folder (eg: Patients) and following their are multiple subfolders, I have to open a specific subfolder out of all the subfolders and so forth until it reaches the data set to retrieve it. . Eg: Patients --> Patient_01 (until patient x) --> MRI --> pre_data --> DICOMS --> [DATA]. Within each subfolder is another subfolder. I know that I will need an if and for loop as there is also a pre data set and a post data set.

If you could help me or guide me on how I could solve this problem. Thank you in advance

Answer 1

[Suraj]

Greetings Samadhi,

It is my understanding that you want to search through all the subfolders of a main folder, and for all DICOM files found, perform some analysis on the data.

You can use "Recursive directory listing - Enhanced RDIR" from the File Exchange to accomplish this. Following is a sample code snippet that demonstrates how to perform a depth-first search through the subfolders of a main folder and loop through DICOM files in each subfolder:

% Define path of the top-level folder
rootFolder = 'C:\Users\JohnDoe\Documents\Patients';

% Perform a depth-first search through the subfolders of the top-level folder
fileList = rdir(fullfile(rootFolder,'**','*.dcm'));

% Loop through each DICOM file found in the subfolders
for i = 1:length(fileList)
    % Get the full path of the DICOM file
    dicomPath = fileList(i).name;
    
    % Read the DICOM file
    dicomData = dicomread(dicomPath);
    
    % Perform some analysis on the DICOM data
    % ...
end

In this code snippet, we first define the path to the top-level folder. We then use the rdir function to perform a depth-first search through all the subfolders of the top-level folder and retrieve a list of all DICOM files found (including those in subfolders). We then loop through each DICOM file in the list and read the data using the dicomread function. Finally, we perform some analysis on the DICOM data (which you can replace with your own analysis code).

You can find more information and examples of using these functions in the following links:

• rdir
• fullfile
• dicomread

Hope this helps!

Regards,

Suraj

[Stephen23]

This answer is very outdated: since R2016b MATLAB's inbuilt DIR has also supported recursive directory searches:

https://www.mathworks.com/help/matlab/ref/dir.html#bsnswnx-1-name

The provided code is also incorrectly commented and contains bugs: for example, this comment

% Get the full path of the DICOM file

is not correct because the following line only returns the filename by itself, not the full path as the comment incorrectly states. We can fix those bugs and also avoid any third-party functions:

P = 'C:\Users\JohnDoe\Documents\Patients';
S = dir(fullfile(P,'**','*.dcm')); % no third-party functions required
for k = 1:numel(S)
    F = fullfile(S(k).folder,S(k).name), % the actual full path
    D = dicomread(F);
    .. etc
end

You know that TMW has badly publicised an improvement when many years later TMW staff are totally unaware of the improvement. Reading the DIR documentation is highly recommended.