<DIV>Hello Luis,</DIV>
<DIV>Thank you very much for your valuable suggestions and inputs.</DIV>
<DIV>Neha<BR><BR><B><I>Luis Ibanez <luis.ibanez@kitware.com></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid"><BR><BR>Hi Neha,<BR><BR><BR>For the same image: tumor57.png you can also use<BR>the ShapeDetectionLevelSetImageFiltere.<BR><BR>Note however that this filter defines the borders<BR>of structures based on gradients. Therefore the<BR>segmentation will find the internal border of the<BR>tumor, if you initialize the level set in the center.<BR><BR>A segmentation of the tumor in tumor57.png is attached.<BR><BR>It was generated with the example in<BR><BR>Insight/Examples/Segmentation/<BR>ShapeDetectionLevelSetFilter<BR><BR>without any modification in the source code, and just<BR>by using the following command line arguments<BR><BR>ShapeDetectionLevelSetFilter<BR>tumor57.png tumor57Segmented.png 30 63 5 1 -1 5 1 20<BR><BR><BR>Where<BR><BR>the number 30 63 are the approximate center of the tumor<BR>the number 5 is the radius to be used for an initial level set<BR>the number 1 is the sigma for
the gaussian used in the speed<BR>image computation<BR>the numbers -1 5 are alpha and beta for the Sigmoid filter used<BR>in the speed image computation<BR>the numbers 1 20 are the curvature and propagation scaling.<BR><BR><BR>For a detailed description of this example, please look at the<BR>ITK Software Guide<BR><BR>http://www.itk.org/ItkSoftwareGuide.pdf<BR><BR>in the Level Set Segmentation Chapter.<BR><BR><BR><BR><BR>On way of getting the external border of the tumor is to dilate<BR>this segmentation, and use it as the inital level set for another<BR>run of the ShapeDetection filter. In this way the level set will<BR>walk up to the next edge.<BR><BR><BR><BR>Regards,<BR><BR><BR><BR>Luis<BR><BR><BR>-----------------<BR>neha k wrote:<BR><BR>> Hello Luis,<BR>> I did not make any changes to code. But I was trying to output image <BR>> mhd & raw format. It is working fine though. Thanks a lot for your input.<BR>> Now, I tried to use shapeDetectionLevelSet Example to
work with Brain <BR>> tumour Raw Image (Attached - tumour57.raw), I am not getting any desired <BR>> result. For such tumor images, do you have any suggestions for what <BR>> Level Set Filter to choose? Smoothing (Curvature Anisotropic diffusion <BR>> Filter) did not seem to help at all. Moreoever, I am not sure why <BR>> result of above smoothing produces output with black border. I have <BR>> attached original Image (tumour57.raw), output of smoothing ( <BR>> tumour57_CurvAnisoSmooth.mhd.raw ) and result of giving this smoothed <BR>> image to Shape Detection Level Set filter ( <BR>> tumour57_CurvAnisoSmooth_LevelSet.raw ).<BR>> Any input on this is appreciated.<BR>> Thanks,<BR>> Neha<BR>> <BR>> */Luis Ibanez <LUIS.IBANEZ@KITWARE.COM>/* wrote:<BR>> <BR>> <BR>> Hi Neah,<BR>> <BR>> Thanks a lot for posting such a detailed message.<BR>> <BR>> <BR>> We attempted to reproduce the result that you reported,<BR>> but the
program worked fine for us.<BR>> <BR>> <BR>> <BR>> Here are the command line parameters that we used,<BR>> and the output from the program:<BR>> <BR>> <BR>> A) Command line:<BR>> <BR>> ShapeDetectionLevelSetFilter BrainT1Slice.png T1.png<BR>> 81 113 5 1 -0.5 3 0.05 1<BR>> <BR>> Output:<BR>> <BR>> Max. no. iterations: 800<BR>> Max. RMS error: 0.02<BR>> <BR>> No. elpased iterations: 108<BR>> RMS change: 0.0199696<BR>> <BR>> <BR>> <BR>> B) Command line:<BR>> <BR>> ShapeDetectionLevelSetFilter BrainProtonDensitySlice.png PD.png<BR>> 81 113 5 1 -0.5 3 0.05 1<BR>> <BR>> Output:<BR>> <BR>> Max. no. iterations: 800<BR>> Max. RMS error: 0.02<BR>> <BR>> No. elpased iterations: 125<BR>> RMS change: 0.0189581<BR>> <BR>> <BR>> The output images (T1.png and PD.png) are attached.<BR>> <BR>> <BR>> <BR>> <BR>> Did you modified th! e code of this Example<BR>> in any way
before running it ?<BR>> <BR>> <BR>> <BR>> Please let us know,<BR>> <BR>> <BR>> Thanks<BR>> <BR>> <BR>> <BR>> Luis<BR>> <BR>> <BR>> --------------------------<BR>> neha k wrote:<BR>> <BR>> > Hello,<BR>> ><BR>> > I am trying to check with<BR>> ITK1.8\Example\ShapeDetectionLevelSetFilter,<BR>> > and do not get desired output. I tried this compiled example with<BR>> > following input images and parameters -<BR>> ><BR>> > *1. BrainT1Slice.png(input image from \ITK\Examples\Data) - with *<BR>> ><BR>> > Seed Point - (81 113) , Distance - 5.0,<BR>> ><BR>> > Sigma SigmoidAlpha SigmoidBeta are -- 1 .0 -0.5 3.0<BR>> ><BR>> > Curv. Scaling -- 0.05 Propogation Scaling -- 1<BR>> ><BR>> > *Output File Name Attached - ShapeDetectionLevelSetFilterOutput4.png*<BR>> ><BR>> > *2. BrainProtonDensitySlice.png with Seed Point - (81,114) and<BR>> rest
of<BR>> > the parameters *have same values as above.<BR>> ><BR>> > Problem - Result of SigmoidFilter is Blank Image while output ! of<BR>> > ShapeDetectionLevelSet Filter for both images is something weird.<BR>> > (attached files)<BR>> ><BR>> > Any input on this appreciated.<BR>> ><BR>> > Thanks,<BR>> ><BR>> > Neha<BR>> ><BR>> ><BR>> ><BR>> <BR>> <BR>> > ATTACHMENT part 2 image/png name=T1.png<BR>> <BR>> <BR>> > ATTACHMENT part 3 image/png name=PD.png<BR>> <BR>> ------------------------------------------------------------------------<BR>> Do you Yahoo!?<BR>> The all-new My Yahoo! <HTTP: my.yahoo.com>– Get yours free!<BR><BR><BR><BR>> ATTACHMENT part 2 image/png name=tumor57SegmentedShapeDetectionLevelSet.png<BR></BLOCKQUOTE><p>
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