[Insight-users] Current state of "Active Contours without edges" in Review folder? - Example?
Amardeep Singh
amar.singh at gmx.de
Tue Jul 28 05:40:37 EDT 2009
Hello everyone
Unfortunately, I have not yet received an answer to my question on how
to interpret the different parameters of
the "Active Contours without edges" algorithm. Has anyone already used
the filter and can share his understanding of
the meaning of the parameters, please?
Thanks a lot!
Best regards
Amardeep
Amardeep Singh wrote:
> 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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