Hi again,<div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<div>I have made some progress on my own by randomly selecting an isovalue of 0.5. Now my level set segmentation is no longer pitted, but it has the same volume in mm^3 as the initially inputted fuzzy connectedness segmentation. It only performed one iteration and the RMS change was 0.0014962. The maximum RMS error was set to 0.002 and the maximum number of iterations was set to 100. The number of diffusion iterations was set to 10, the diffusion conductance was set to 2.0, the propagation weight was set to 1.0, the initial model isovalue was set to 0.5, and the maximum number of iterations was set to 100.</div>
<div> </div>
<div></div><div>Any further advice is welcome.<br></div>
<div> <br></div></blockquote><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Thanks,</div>
<div></div></blockquote><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>John<font color="#888888"><br></font></div></blockquote>
<div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><font color="#888888"></font></div><div><div></div><div class="h5">
<div class="gmail_quote">On Thu, Feb 3, 2011 at 12:11 PM, John Drozd <span dir="ltr"><<a href="mailto:john.drozd@gmail.com" target="_blank">john.drozd@gmail.com</a>></span> wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;" class="gmail_quote">
<div>Hello,<br clear="all"></div>
<div>I have performed a reasonable fuzzy connectedness segmentation (that I modified to use multiple seeds) of lateral human brain ventricles in an MRI brain image of a mildly cognitive impaired person that I obtained from the ADNI database.</div>
<div>Prior to performing the fuzzy connectedness segmentation, I smoothed the noise and enhanced the edges using an Anisotropic Diffusion filter.</div>
<div>I am trying to use this fuzzy connectedness segmentation as my initial level set for a level set segmentation but when performing a Laplacian Level Set segmentation, I get a pitted volume.</div>
<div>I think the following are my problems.</div>
<div>1) When I load the label map from the fuzzy connectedness segmentation into 3D Slicer to view it, I get Fg: None and Bg: 1 for the segmented volume, and Fg: None and Bg: 0 for the black area that surrounds the ventricles. I think that I am setting my foreground and background values incorrectly. I feel this is a problem because I need to specify an isovalue midway between the foreground and background values. I can send you my fuzzy connectedness and Laplacian level set segmentation code if this would help you be able to help me. Also, the laplacian level set segmentation performs anisotropic diffusion. Because I perform this prior to my fuzzy connectedness segmentation, I am essentially performing anisotropic diffusion twice. Could this be a problem?</div>
<div>2) Also, how do you run the level set segmentation to go to convergence. Do you just input a large maximum number of iterations?</div>
<div>3) Also how can I use the outputted "speedImage.mha" figure to help me tune my parameters for "DiffusionIterations", "DiffusionConductance", "PropagationWeight", "InitialModelIsovalue" and "MaximumIterations". I can send you the speed image as well.</div>
<div>4) Also, the level set segmentation only performs 1 iteration eventhough I specified a maximum 100 iterations. Should I use a smaller RMS error than 0.002?</div>
<div> </div>
<div>Any help would be appreciated.</div>
<div> </div>
<div>Thanks for your time,</div>
<div> </div>
<div>John</div>
<div><br>-- <br></div>
<div>John Drozd<br></div>
<div>Post-Doctoral Fellow, Robarts Research Institute</div>
<div>The University of Western Ontario</div>
<div>London, ON, Canada<br></div><br></blockquote></div><br><br clear="all"><br>-- <br>
<div>John Drozd<br></div>
<div>Post-Doctoral Fellow, Robarts Research Institute</div>
<div>The University of Western Ontario</div>
<div>London, ON, Canada<br></div><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br><div>John Drozd<br></div>
<div>Post-Doctoral Fellow, Robarts Research Institute</div>
<div>The University of Western Ontario</div>
<div>London, ON, Canada<br></div>
<br>