Watershed Segmentation is resulting in more segments than necessary. How can I change this?

I have a ground truth image and I want to find its skeleton points and from these skeleton points I want to use watershed to recreate the ground truth image.

The problem is, when I use bwmorph(skel), the skeleton points touch each other and it results in an under segmented image. I tried to erode the image before I find the skeleton points, and this resulted in oversegmentation. The code and images are below:

img = imread('181091.jpg');
img = double(img);
seg = readSeg('181091.seg');

R = img(:,:,1);
G = img(:,:,2);
B = img(:,:,3);

[GxR,GyR] = gradient(R);
[GxG,GyG] = gradient(G);
[GxB,GyB] = gradient(B);

Grad = sqrt(GxR.^2 + GyR.^2 + GxG.^2 + GyG.^2 + GxB.^2 +GyB.^2);

img_skel = 0;

for i = 1:max(max(seg))
    seg_sel = seg==(i);
    seg_sel = imerode(seg_sel,ones(3,3));
    img_skel1 = bwmorph(seg_sel,'skel',inf);
    img_skel = img_skel + img_skel1;
end
figure, imagesc(img_skel)

watersh = imimposemin(Grad,img_skel);
Labels = watershed(watersh);
Labels = label2rgb(Labels);

The ground truth has 6 segments:

However, my result (with imerode, bwmorph, imimposemin and watershed) has 14 segments:

I want to be able to have the same number of segments. What could I add or change in my code? If I don't use imerode, the image looks like this:

Answer 1

[Image Analyst]

Try this instead:

DEM in the File Exchange

[Ruba]

Thank you Image Analyst for your suggestion.

Unfortunately, this code is for a project I'm working on with a professor and it has to be written by myself and I can't use some one else's code. I just need help figuring out a way to improve what I already wrote

[Image Analyst]

OK, here are some links to help you:

http://www.mathworks.com/help/images/examples/marker-controlled-watershed-segmentation.html

http://blogs.mathworks.com/steve/2013/11/19/watershed-transform-question-from-tech-support/

http://cmm.ensmp.fr/~beucher/wtshed.html