Looping Through Multiple Paths

I am trying to create a code that runs through multiple paths/different folders, within one large mother directory. The folders have the names Users 1, Users 2, Users 3, etc in the mother directory Group Analysis. I want to go 7 subfolders below Users 1, etc. I then want to create a for loop in which I execute commands in each of the subfolders consecutively. I have only successfully wrote a program for one path only:

s= {

{'/Users/Naomi/Desktop/GroupAnalysis/Users/jk/Documents/LongitudinalR01/Imaging/raw/c001/s1/0007_t1_mpr_AX_MPRAGE'},

s_out = {'/Users/Naomi/Desktop/output'};

for kk = 1:numel(s);

t = spm_select('FPList', (kk), '.*');
hdr = spm_dicom_headers(t);
spm_dicom_convert(hdr, 'all', 'flat', 'nii', char(s_out(kk)))

end

Thanks!!

Answer 1

[ag]

Hi Naomi,

To process multiple directories within a "mother directory" and executing commands in each of the subfolders consecutively, you can use the MATLAB function "dir" to list all directories within and then execute the respective commands.

The below code snippet demonstrates how to achieve the same:

% Get a list of all user directories in the motherDir
userDirs = dir(fullfile(motherDir, 'Users*'));

% Loop over each user directory
for i = 1:length(userDirs)
    if userDirs(i).isdir
        userDirPath = fullfile(motherDir, userDirs(i).name);
        
        % Navigate 7 subfolders deep
        subDirPath = fullfile(userDirPath, 'jk/Documents/LongitudinalR01/Imaging/raw/c001/s1/0007_t1_mpr_AX_MPRAGE');
        
        % Check if the subdirectory exists
        if isfolder(subDirPath)
            % Define the output directory
            s_out = '/Users/Naomi/Desktop/output';
            
            % Execute the respective command in the subdirectory, subDirPath
        end
    end
end

For more details, please refer to the following MathWorks documentations:

• dir - https://www.mathworks.com/help/matlab/ref/dir.html
• fullfile - https://www.mathworks.com/help/matlab/ref/fullfile.html
• isfolder - https://www.mathworks.com/help/matlab/ref/isfolder.html

Hope this helps!