[Insight-users] Re: Brain Tumor + Level Set Filter
Luis Ibanez
luis.ibanez at kitware.com
Fri Dec 3 21:13:43 EST 2004
Hi Neha,
What version of ITK are you using ?
You are probably using the ITK version that used to read the PNG
images inverting the Y access, and therefore the position of the
pixel (30,63) is no longer the center of the tumor.
What are you using to read the Raw image into ITK ?
Did you changes the pixel types in the code in order to match the
input image ?
The parameters of a segmentation method are specific for the input
pixel type, the image modality and the anatomical structures that
you plan to segment.
Please make available the original raw image.
Thanks
Luis
----------------
neha k wrote:
> Hello Luis,
> Thanks for the reply. I have chanegd interataions to 100. But with
> same png image, I get different result (I have used ctr. as(79,93). The
> center that you have specified (30,63) seems to be out of brain area.
> Also, if i use original raw image, output is blank. I am not sure what
> is going wrong. (I saved original raw image as .png image by making it
> 8-bits per channel from 16-bit per channel in photoshop , and then sent
> to you)
> Neha.
>
> */Luis Ibanez <luis.ibanez at kitware.com>/* wrote:
>
>
> Hi Neha,
>
> Thanks for posting your image.
>
> The ThresholdSegmentationLevelSet worked fine in this image,
>
> I used the example code in:
>
>
> Insight/Examples/Segmentation/
> ThresholdSegmentationLevelSetImageFilter.cxx
>
>
> Just replaced the maximum number of iteration in line 200.
>
> The current value is 1200 iteration,
> you must use here 100 iterations.
>
>
> Then in the command line use
>
>
> ThresholdSegmentationLevelSetImageFilter
> tumor57.png segmented.png 30 63 5 70 207
>
>
> (in a single command line)
>
> The numbers: 30 63 are respectively the X,Y approximate coordinates
> of the tumor center.
>
> The number: 5 is a radius to be used for creating a initial level set
> as a circle of radius 5 pixels centered at (30,63).
>
> The numbers: 70 and 207 and the lower and upper thresholds that define
> a borde! r for the tumor.
>
>
>
> In the future you may find useful to use the interactive application
>
>
> InsightApplications/
> ThresholdSegmentationLevelSetFltkGui
>
>
> That allows you to set all this parameters interactively and see the
> evolution of the level set iteration by iteration.
>
> Note that it is *very* important to monitor/supervise the level set
> because if you run it for too few iterations the tumor will be under
> segmented, an if you run it for too many, the level set will leak and
> start invading other brain structures.
>
> Looking at the level set as it is evolving is the best way to figure
> out how many iterations are enough for stopping the level set.
>
> By fine tunning the values of the lower/upper thresholds, the curvature
> scaling and the number of iterations you will be able to refine the
> borders of the segmented region.
>
> You could also post-process the segmented image with a filter such as
> the BinaryMedianImage! Filter or the new itkVotingBinaryImageFilter.
>
>
>
> Please find attached the PNG image with the tumor segmented from your
> image.
>
>
>
> Regards,
>
>
> Luis
>
>
>
> ---------------------------------------------------------------------------
> neha k wrote:
>
> > Hello Luis,
> >
> > Thanks for your reply. While using this filter, with my Brain tumor
> > Image attached, I am not getting any luck with application, i
> have tried
> > different parameter values.
> > I am not sure what Level Set filters would be good to delineate
> tumor in
> > my image attached. Smoothing did not seem to help for using
> > ThresholdLevelSet and ShapeDetection Level Set. My original Image is
> > RAW with .mhd header file.
> > Any suggestions? How can I tune pramaters to separate tumor? What
> type
> > of preprocessing and other filters might help?
> >
> > Thanks,
> > Neha
> >
> > */Luis Ibanez /* wrote:
> >
> >
> > Hi Neah,
> >
> > Thanks a lot for posting such a detailed message.
> >
> >
> > We attempted to reproduce the result that you reported,
> > but the program worked fine for us.
> >
> >
> >
> > Here are the command line parameters that we used,
> > and the output from the program:
> >
> >
> > A) Command line:
> >
> > ShapeDetectionLevelSetFilter BrainT1Slice.png T1.png
> > 81 113 5 1 -0.5 3 0.05 1
> >
> > Output:
> >
> > Max. no. iterations: 800
> > Max. RMS error: 0.02
> >
> > No. elpased iterations: 108
> > RMS change: 0.0199696
> >
> >
> >
> > B) Command line:
> >
> > ShapeDetectionLevelSetFilter BrainProtonDensitySlice.png PD.png
> > 81 113 5 1 -0.5 3 0.05 1
> >
> > Output:
> >
> > Max. no. iterations: 800
> > Max. RMS error: 0.02
> >
> > No! . elpased iterations: 125
> > RMS change: 0.0189581
> >
> >
> > The output images (T1.png and PD.png) are attached.
> >
> >
> >
> >
> > Did you modified th! e code of this Example
> > in any way before running it ?
> >
> >
> >
> > Please let us know,
> >
> >
> > Thanks
> >
> >
> >
> > Luis
> >
> >
> > --------------------------
> > neha k wrote:
> >
> > > Hello,
> > >
> > > I am trying to check with
> > ITK1.8\Example\ShapeDetectionLevelSetFilter,
> > > and do not get desired output. I tried this compiled example with
> > > following input images and parameters -
> > >
> > > *1. BrainT1Slice.png(input image from \ITK\Examples\Data) - with *
> > >
> > > Seed Point - (81 113) , Distance - 5.0,
> > >
> > > Sigma SigmoidAlpha SigmoidBeta are -- 1 .0 -0.5 3.0
> > >
> > > Curv.! Scaling -- 0.05 Propogation Scaling -- 1
> > >
> > > *Output File Name Attached -
> ShapeDetectionLevelSetFilterOutput4.png*
> > >
> > > *2. BrainProtonDensitySlice.png with Seed Point - (81,114) and
> > rest of
> > > the parameters *have same values as above.
> > >
> > > Problem - Result of SigmoidFilter is Blank Image while output ! of
> > > ShapeDetectionLevelSet Filter for both images is something weird.
> > > (attached files)
> > >
> > > Any input on this appreciated.
> > >
> > > Thanks,
> > >
> > > Neha
> > >
> > >
> > >
> >
> >
> > > ATTACHMENT part 2 image/png name=T1.png
> >
> >
> > > ATTACHMENT part 3 image/png name=PD.png
> >
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> >
>
>
>
> > ATTACHMENT part 2 image/png name=tumor57Segmented.png
> *
>
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