Here's the updated code for everything I have thusfar. I still have the same problem as listed above though.
% % % % % Color presence in Turtle Shell % % % % %
% % % Finding the Area of the Shell % % %
function g = img2rat(k)
% % % reads and crops % % %
f = imread(k);
g = imcrop(f,[750 500 1800 1300]);
figure, imshow(g); title ('Cropped Image');
% % % Converts to BW Image to fill shell and cut out parts that are not shell % % %
burnedImage = g;
BW = im2bw(burnedImage, .5); % converts the truecolor image RGB to a binary image %
BW=~BW; % Inverse of the BW image %
filled = imfill(BW, 'holes'); % Fills the holes of the shell %
filled=~filled; % Inverse of the filled image %
figure, imshow(filled); title('Filled Black and White Image');
% % % DRAW LINES % % %
burnedImage = filled;
% % % Line1 % % %
hLine = imline();
binaryImage1 = hLine.createMask();
burnedImage(binaryImage1) = 255;
imshow(burnedImage); title('BurnedImage1');
% % % Line2 % % %
hLine=imline();
binaryImage2 = hLine.createMask();
burnedImage(binaryImage2) = 255;
imshow(burnedImage); title('BurnedImage2');
% % % Line3 % % %
hLine=imline();
binaryImage3 = hLine.createMask();
burnedImage(binaryImage3) = 255;
imshow(burnedImage); title('BurnedImage3');
% % % Line4 % % %
hLine=imline();
binaryImage4 = hLine.createMask();
burnedImage(binaryImage4) = 255;
imshow(burnedImage); title('BurnedImage4');
% % % Line5 % % %
hLine=imline();
binaryImage5 = hLine.createMask();
burnedImage(binaryImage5) = 255;
imshow(burnedImage); title('BurnedImage5');
set( findobj(gcf,'type','line'), 'LineWidth', 500);
burnedImage = ~burnedImage; % Have to take the inverse so shell area and not background is whtie.
figure, imshow(burnedImage); title('Image for Analysis');
% % % Find Area of each Region % % %
burnedImage = bwareaopen(burnedImage, 100);
STATS = regionprops(burnedImage, 'Area');
allArea = [STATS.Area] % Only displays the largest area.
And then the code continues but im having a problem with the above (dashed lines appear).