function [DTItracts] = MuscleParameters_Deterministic(muscle_path,order,apo_line)

% ----------------- INPUT -----------------
% muscle_path: string of pathway directory for muscle of interest (EX: 'FCU')
% order: order of polynomial fitting (EX: 2)
% apo_line: vector (2x3 matrix of 3D coordinates) of aponeurosis in that muscle (EX: [3 4 5; 6 7 8]) 

% ----------------- OUTPUT -----------------
% DTItracts: structure with the fields:
%     - M: the generated number of tracts
%     - nan_rows: logical array for rows (samples) that were eliminated due to non-tracking or low intensity
%     - overall_anat_length: Mx2 vector of actual lengths of each m-th fiber (2nd col) (1st col = fiber index)
%     - max_intensity: Mx2 vector of actual lengths of each m-th fiber (2nd col) (1st col = fiber index)
%     - anat_coord: Mx1 vector of anatomical space coordinates for each m-th fiber
%     - tracts_xyz: 3x(n*M) array of all points of all fibers (anatomical space)
%     - fibindex: Mx2 array of start index and end index (in tracts_xyz) of each m-th fiber
%     - tracts_xyz_dti: 3x(n*M) array of all points of all fibers (DTI space)
%     - fibindex_dti: Mx2 array of start index and end index (in tracts_xyz) of each m-th fiber (DTI space)
%     - est_anat_length: Mx2 vector of polynomial-estimated lengths of each m-th fiber (2nd col) (1st col = fiber index)
%     - num_pts: Mx2 vector of number of points used in fitting (2nd col) (1st col = fiber index)
%     - PolyCoeff: has substructures x,y,z,t0,t1 --> polynomial fit coefficients
%     - RSQ: Mx3 array, col 1 = x R^2 value, col 2 = y R^2 value, col 3 = z R^2 value
%     - RSQ_adj: Mx3 array, col 1 = x adjusted R^2 value, col 2 = y adjusted R^2 value, col 3 = z adjusted R^2 value
%     - RMSE: Mx1 array, RMSE value of m-th fiber
%     - curvature: Mx1 vector with curvature for each m-th fiber
%     - penangle: Mx1 vector with pennation angles for each m-th fiber
%     - FA,AD,MD,RD: each is Mx1 vector of average diffusivity for each m-th fiber
%     - inflection_loc = Mx1 cell with t location of inflection points of each m-th fibers
%     - inflection_pts = Mx1 cell with number of inflection points of each of m-th fibers

% ----------------- NOTE -----------------
% run in pathway describing the limb that contains the directory of muscle being analyzed (EX. run this in 'DominantLower' folder)

%% Set Up Structure

% Define structure and save each parameter used
DTItracts = struct;

% Define variables using inputs
DTItracts.order = order;                            % polynomial order for fitting
tracts_path = strcat(muscle_path);                  % tracts_path: string of pathway directory of where the tracked files are located (EX: 'FCU')

%% Extrapolate Coordinates and Make Arrays with Points

fprintf('Finding coordinates and making structures for tracts in: %s...\n',tracts_path);
[DTItracts,M,nan_rows] = FindCoordinates_Deterministic(DTItracts,tracts_path);      % Extract coordinates from raw tracts, save valid tracts to structures
disp('Coordinates saved.');

%% Find Diffusivity Values

fprintf('Reading Diffusivity Values for tracts in: %s...\n',tracts_path);
[DTItracts] = ReadDiffusivity_Deterministic(DTItracts,tracts_path,nan_rows);      % Calculate diffusivity metrics for each tract
disp('Diffusivity values saved.'); 

%% Perform Polynomial Fitting

fprintf('Performing polynomial fit for tracts in: %s...\n',tracts_path);
[DTItracts] = LSQ_Polynomial(DTItracts,order,M);                    % Fit polynomial curve of given order to each tract
disp('Polynomial fitting complete.'); 

%% Find Pennation Angles

pointA = apo_line(1,:);     % Save starting point of aponeurosis
pointB = apo_line(2,:);     % Save ending point of aponeurosis

fprintf('Finding pennation angles for tracts in: %s...\n',tracts_path);
[DTItracts] = FindPennation_Deterministic(DTItracts,M,pointA,pointB);             % Find pennation angle of each tract using the points from the aponeurosis vector
disp('Pennation angles calculated.');                                    

%% Find Curvature

fprintf('Finding curvature values for tracts in: %s...\n',tracts_path);
[DTItracts] = FindCurvature(DTItracts,M);                           % Find curvature of each tract
disp('Curvature calculated.');

%% Find Inflection Points

fprintf('Finding inflection points for tracts in: %s...\n',tracts_path);
[DTItracts] = FindInflection(DTItracts,M);                          % Find "inflection points" (S-shapes, concave to convex) of each tract
disp('Inflection points calculated.');

%% Muscle Parameters Calculated

disp('Muscle Parameter Calculations DONE!');

end