[Insight-users] Current state of "Active Contours without edges" in Review folder? - Example?
Amardeep Singh
amar.singh at gmx.de
Thu Jul 23 10:33:55 EDT 2009
Dear Kishore
Thanks a lot for the bugfix. I can get the program to run with the
newest fix.
However, I would be interested in the parameters that you used in order
to produce the result.
Could you give me a little more insight in the meaning of some of the
parameters, as well,please?
Some are quite clear, but I couldn't find a correspondence for the
others in the paper:
1. CurvatureWeight: Penalize high curvature of level set?; where is this
in the paper?
2. AreaWeight: Penalize high area of level set surface
3. ReinitializationWeight, in the code also called
"SetReinitializationSmoothingWeight":
What does this mean? Is it in the paper?
4. VolumeWeight, in the code also called VolumeMatchingWeight:
What does it mean? Is it in the paper?
5. Volume: I guess that this the parameter of the volume
parametrization, so it penalizes large volumes
within the level set surface.
Thank you very much!
Best regards
Amardeep
Kishore Mosaliganti wrote:
> Hi Amardeep,
>
> Thanks for the format conversion and also for putting up your data. I
> was able to reproduce the problem at my end. Your images had a
> negative origin and revealed a bug in code. This has been corrected
> now in the latest CVS repository.
>
> Meanwhile, I have placed an example script and its output:
> http://bmi.osu.edu/~kishore/Amardeep/
> <http://bmi.osu.edu/%7Ekishore/Amardeep/>
>
> Please try it out at your end and let me know how things work out.
>
> Kishore
>
> On Wed, Jul 22, 2009 at 5:41 AM, Amardeep Singh <amar.singh at gmx.de
> <mailto:amar.singh at gmx.de>> wrote:
>
> Dear Kishore
>
> I have converted the images to *.mhd, just like Alexander
> suggested. Does this solve the issue of
> opening the images for you?
> Please let me know if you still cannot use them.
> Thanks a lot for your help!
>
> Best regards
> Amardeep
>
>
> Oleksandr Dzyubak wrote:
>
> Hi Kishore,
>
> You probably have some box with ITK installed.
> If you do, you could compile examples from ITK which
> comes in separate package "InsightApplications" (if you have
> not done so yet).
> Once successfully compiled, under directory
> ~/InsightApplications/ConvertBetweenFileFormats you can find
> the executable
> ConvertBetweenFileFormats.
>
> The rest is quite simple. If you want to use Paraview, do as below
>
> ./ConvertBetweenFileFormats image.nii image.mhd
>
> The second operand could be change to whatever your favorite
> format is.
>
> Alex
>
> Kishore Mosaliganti wrote:
>
> Hi Amardeep,
>
> I am unable to open your images correctly or something is
> wrong.. What I saw was that the images was having 0s
> throughout.
>
> Can you write them in some other format that I can open in
> Paraview, for example?
>
> Thanks,
> Kishore
>
> On Tue, Jul 21, 2009 at 2:06 PM, Amardeep Singh
> <amar.singh at gmx.de <mailto:amar.singh at gmx.de>
> <mailto:amar.singh at gmx.de <mailto:amar.singh at gmx.de>>> wrote:
>
> Dear Kishore
> Dear ITK Users
>
> I have now been trying to use the filter, but,
> unfortunately, I
> cannot get it to run. My initial level set and my
> feature image
> are overlapping perfectly (same orientation/position
> information
> in the headers), but when I run the example program
> "ScalarSinglePhase3DTest.cc", I get the following error
> (it is
> indeed printed out twice):
> Exception caught !
>
> itk::ExceptionObject (0x8152b00)
> Location: "virtual void
> itk::DataObject::PropagateRequestedRegion()"
> File:
>
> /asingh/workspace/InsightToolkit-3.14.0/Code/Common/itkDataObject.cxx
> Line: 397
> Description: Requested region is (at least partially)
> outside the
> largest possible region.
>
>
> Exception caught !
>
> itk::ExceptionObject (0x8149d88)
> Location: "virtual void
> itk::DataObject::PropagateRequestedRegion()"
> File:
>
> /asingh/workspace/InsightToolkit-3.14.0/Code/Common/itkDataObject.cxx
> Line: 397
> Description: Requested region is (at least partially)
> outside the
> largest possible region.
>
> My parameters are chosen arbitrarily:
> curvature weight: 0.1
> area weight: 0.1
> laplacian weight: 0.1
> volume weight: 0.1 (what does this mean?)
> volume: 0 (what does this mean?)
> overlap weight: 0
>
> For your convenience, I have made the images available
> under the
> following URL:
> http://www.doc.ic.ac.uk/~asingh/
> <http://www.doc.ic.ac.uk/%7Easingh/>
> <http://www.doc.ic.ac.uk/%7Easingh/>
>
> I have also put my code there.
>
> Does anyone have an idea, why it fails?
>
> Any comment is highly appreciated!
>
>
> Best regards
> Amardeep
>
>
> Kishore Mosaliganti wrote:
>
> Hi Amardeep,
>
> The names of the classes were changed when moving
> to the
> Review directory. Therefore, you will need to
> modify the main
> cxx that you downloaded from Insight Journal.
>
> Thanks,
> Kishore
>
> On Thu, Jul 16, 2009 at 11:17 AM, Amardeep Singh
> <amar.singh at gmx.de <mailto:amar.singh at gmx.de>
> <mailto:amar.singh at gmx.de <mailto:amar.singh at gmx.de>>
> <mailto:amar.singh at gmx.de
> <mailto:amar.singh at gmx.de> <mailto:amar.singh at gmx.de
> <mailto:amar.singh at gmx.de>>>> wrote:
>
> Dear ITK Users
>
> I would like to use the "Active Contours without
> edges"
> algorithm,
> which is available in
> the Review directory if I understood correctly.
> So, I am wondering where I can find an example
> about how to use
> the algorithm. I tried to run the
> "ScalarSinglePhase3DTest" example of the Insight
> Journal
> submission, but it failed to compile.
> The first error read:
> /applications/ScalarSinglePhase3DTest.cc:4:52:
> error:
> itkSparseMultiphaseLevelSetImageFilter.h: No
> such file or
> directory
>
> I am a little confused by the multitudes of
> implementations
> that
> are available with respect to this
> algorithm, at the moment (3 Insight Journal
> submission +
> Review).
> Can someone tell me where to start and how to
> get it running?
> Thanks a lot!
>
> Best regards
> Amardeep
>
>
>
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