[Insight-users] Current state of "Active Contours without edges" in Review folder? - Example?
Amardeep Singh
amar.singh at gmx.de
Tue Jul 28 10:31:31 EDT 2009
Dear Kishore
Thank you so much for your detailed answer. This is still helpful, even
though it is explained in your last Insight paper.
I must have missed that - Sorry!
Best regards
Amardeep
Kishore Mosaliganti wrote:
> Dear Amardeep,
>
> Please take a look at the Insight Journal publication:
>
> http://www.insight-journal.org/browse/publication/642
>
> All the parameters that you mentioned below are completely explained
> in the context of the level-set PDE that was implemented. If you want
> to know more about the mathematics , the Insight paper further
> references the following papers:
>
> 1. T. Chan and L. Vese. An active contour model without edges. In
> Scale-Space Theories in Computer Vision, pages 141–151, 1999.
> 2. A. Dufour, V. Shinin, S. Tajbakhsh, N. Guillen-Aghion, J. C.
> Olivo-Marin, and C. Zimmer. Segmenting and tracking fluorescent cells
> in dynamic 3-d microscopy with coupled active surfaces. Image
> Processing, IEEE Transactions on, 14(9):1396–1410, 2005.
>
> Finally, the parameter m_ReinitializationWeight which was added
> recently is by incorporating the method explained in the paper:
> 3. Chunming Li, Chenyang Xu, Changfeng Gui, and Martin D. Fox, "Level
> Set Evolution Without Re-initialization: A New Variational
> Formulation",/ CVPR 2005/.
>
> In Insight/Examples/Review, we have placed fully commented example
> codes for using the filters -- both dense and sparse for the single
> phase cases.
>
> Here, I explain the parameters once again:
>
> 1. CurvatureWeight - Penalize high curvatures of level set curve or
> surface. This also means that if your object to be segmented has small
> features on its boundaries, then they will be missed.
> 2. AreaWeight - Hastens the movement of level-set to its final
> convergence. If you initialized in a mostly interior region, then this
> parameter must be negative to force the level-set to grow quickly and
> vice-versa.
> 3. ReinitializationWeight - This is based on reference 3 above. It
> forces the level-set function to remain a signed distance function as
> it evolves. You can turn it off (set to 0) in the sparse-field methods
> since the sparse implementation is not based on a signed distance
> function. Only needs to be used in dense implementation.
> 4. VolumeWeight - In tracking applications, this will weight the
> volume term for the object being tracked.
> 5. Volume - The volume of the object being tracked in terms of pixels.
>
>
> Kishore
>
>
>
> Finally, please keep checking the CVS version of the code regularly
> for getting the latest updates.
>
> Kishore
>
>
>
> On Tue, Jul 28, 2009 at 5:40 AM, Amardeep Singh <amar.singh at gmx.de
> <mailto:amar.singh at gmx.de>> wrote:
>
> 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/>
> <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>
> <mailto: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>>
> <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 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/>
> <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>>>
> <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
> <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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