[Insight-users] Re: Brain Tumor + Level Set Filter
Luis Ibanez
luis.ibanez at kitware.com
Wed Dec 22 22:45:13 EST 2004
Hi Neha,
Thanks for posting the .zip file with your image.
The problem is that you specified the endianess
incorrectly in the MetaImage header.
You have now
BinaryDataByteOrderMSB = True
but you should have
BinaryDataByteOrderMSB = False
Simply displaying the image exposes this error, because
you can see how the pixels on high intensity get saturated
and wrapped.
Regards,
Luis
-------------
neha k wrote:
> Hello Luis,
>
> I am using ITK 1.8. I did not change pixel type. (They are read as -
> float in the program )
> Also, my original image is RAW - 256 * 256, Signed-Short, Big Endian.
> I read the image as .mhd format. Please find original image attached.
>
> Thanks,
> Neha
>
> */Luis Ibanez <luis.ibanez at kitware.com>/* wrote:
>
>
> 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
> &! gt; 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 /* 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 l! ot 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(in! put 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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