I understand you want to save your final images in a separate folder in the current folder with names similar to the original PNG files. You can do so by combining both the for loops, using split and concatenation to get your output file names as intended and using imwrite to save them to your new folder
Based on your screenshot, I have assumed your code is in the same file as all your png files and that you want to create a new folder within the current folder
I am attaching your code below with these changes
clear;
Files = dir('*.png');
mkdir 'Masked Glass Brains (Controls)'
Controls_Results_Structure = struct('BW',[],'maskedRGBImage',[]);
for i = 1:length(Files)
RGB = imread(Files(i).name);
[Output_BW, Output_maskedRGBImage] = GlassBrainMask(RGB);
Controls_Results_Structure(i).BW = Output_BW;
Controls_Results_Structure(i).maskedRGBImage = Output_maskedRGBImage;
% Create file name and save to directory
name = split(Files(i).name);
filename = ['Masked ', name{1}, ' ', name{2}];
imwrite(Output_BW,['Masked Glass Brains (Controls)\',filename]);
end
save("Controls_Results_Structure")
