saving an output with loop

I have three subject-specific subdirectories (sub-CC121428, ...) in a main directory, 'diffusion'. I have written a `for` loop to convert a .nii file in each subdirectory to a .mat file:

practice_dir = 'C:\Work\FSL\shared\NCCN_project\diffusion'; %
subjects = [121428 420433 710429]; %

for  n=1:length(subjects)
i = subjects(n);
subname = sprintf('sub-CC%06d',i);
fname_eddy = fullfile(practice_dir,subname,'dwi',sprintf('eddy_output.nii',subname)); 
fname_mask = fullfile(practice_dir,subname,'dwi',sprintf('b0_0.3_mask.nii',subname)); 
CreateROI(fname_eddy, fname_mask, 'NODDI_roi.mat') 
end

The output is saved in the first subject subdirectory and is overwritten with each iteration. How do I save the output of each iteration (NODDI_roi.mat) in the correct subject subdirectory?

[infinity]

Hello,

Did you try to put the path before "NODDI_roi.mat" like

your_sub_direct_file = fullfile(practice_dir,subname,'dwi','NODDI_roi.mat');

Then, you just save your data to this path like

CreateROI(fname_eddy, fname_mask, your_sub_direct_file) 

Answer 1

[Mario Chiappelli]

Save the ouput in an array based off of what iteration you are on. Something like this:

outputArray = string(length(subjects));        % I assume your output is a string
for n = 1:length(subjects)
    % your code
    outputArray(n) = CreateROI(fname_eddy, fname_mask, 'NODDI_roi.mat');
end

Hope this helps :)