[Insight-users] Current state of "Active Contours without edges" in Review folder? - Example?
Kishore Mosaliganti
kishoreraom at gmail.com
Wed Jul 22 22:14:48 EDT 2009
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/
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> 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>> 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>>> 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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