looping though multiple sub-directories

I would like to recursively proces files in subdirectories using MATLAB. I have three subject-specific subdirectories (sub_001, sub_002, sub_003) in a main directory, A, each of which contains a .nii file, B.

In linux, this is possible using a for loop with a .txt file containg a listing of the main directory. For example:

for i in `cat list.txt`; do mv /A/$i/B /path/to/new/destination; done

Can the same be acheived in MATLAB? Essentially, the only thing that needs to change in each iteration is the subject's directory.

Thank you,

Ben

Answer 1

[Rik]

Yes, you just need to load your text file with your paths, and then loop over the contents. If you need help with loading the text file, you can post an example.

[Ben]

I don't understand how to load the .txt file with the path. I can't find reference to this online.

[Rik]

Reading a file is not a difficult task in Matlab. If you Google it you're bound to find dozens of examples. If you use a function like my readfile FEX submission, then you can use the resulting cell array directly in a loop.

You can also directly read all nii files with the code Jan showed you.

Answer 2

[Jan]

FileList = dir('C:\Base\Folder\**\*.nii');
for k = 1:numel(FileList)
    File = fullfile(FileList(k).folder, FileList(k).name);
    ...
end