function MakeSeedpoints(seedmask_name,seedpoints_name,seedpoints_idx_name,ds_factor)

% ----------------- USAGE -----------------
% run this in the muscle folder via terminal/commandline
%       in muscle folder, should be segmentations folder

% ----------------- ARGUMENTS -----------------
% seedmask_name: string of desired seedmask .nii file and path(EX: 'muscle_seedmask.nii.gz')
% seedpoints_name: string of desired seedpoints .txt file and path (EX: 'muscle_seedpoints.txt')
% seedpoints_idx_name: string of desired seedpoints .txt file and path (EX: 'muscle_seedpoints_idx.txt')
% ds_factor: how much to downsample the seedmask voxels by (EX: 2)

% ----------------- OUTPUTS ----------------
% seedpoints_name: a .txt file to be imported into FSL for tractography (EX: 'muscle_seedpoints.txt')
% seedpoints_name_idx: a .txt file to be imported into FSL for tractography (EX: 'muscle_seedpoints_idx.txt')

%% Extract Voxel Coordinates from Seed Mask
fprintf('Creating array of all non-zero voxels in given seedmask: %s...\n',seedmask_name);

% Load NIFTI Images
seed_img = load_untouch_nii(seedmask_name);     % Load the seed mask as a NIFTI structure
seedmask = seed_img.img;                        % Get the image from the structure

% Find Coordinates
idx = find(seedmask);                               % Find linear indices of all NON-ZERO intensity values
[row, col, slice] = ind2sub(size(seedmask),idx);    % Separate indices to subscripts to find x,y,z
fibnr = find(row(:));                               % Find the index number for the coordinate
seedpoints = [fibnr(:), row(:), col(:), slice(:)];  % Create4 an Nx4 matrix with coordinates of all voxels in seedmask (n,x,y,z)

%% Save Seedpoint Text Files

% Downsample the Seedpoints by Given Factor
seedpoints_ds = downsample(seedpoints,ds_factor);   % Downsample the seedpoints by factor - don't need contiguous voxels
seedpoints_ds_no_idx = seedpoints_ds(:,2:4);        % Same downsampling for file without indices

% Save Seedpoints File with No Index
writematrix(seedpoints_ds_no_idx,seedpoints_name,'Delimiter','space');  % save as .txt file to import into FSL commands
    % N = number of rows = total number of voxels the mask contains
    % x = column 1 = x-coordinates in diffusion MRI space
    % y = column 2 = y-coordinates in diffusion MRI space
    % z = column 3 = z-coordinates in diffusion MRI space
fprintf('Seedpoint array saved as %s\n',seedpoints_name);

% Save Seedpoints File with Index
seedpoints_ds_idx = seedpoints_ds;
j = find(seedpoints_ds(:,1));
seedpoints_ds_idx(:,1) = j;
writematrix(seedpoints_ds_idx,seedpoints_idx_name,'Delimiter','space'); % save as .txt file to import into FSL commands
    % N = number of rows = total number of voxels the mask contains
    % n = column 1 = seedpoint/fiber number
    % x = column 2 = x-coordinates in diffusion MRI space
    % y = column 3 = y-coordinates in diffusion MRI space
    % z = column 4 = z-coordinates in diffusion MRI space
fprintf('Seedpoint indexed array saved as %s\n',seedpoints_idx_name);

exit;

end