[Insight-users] Obtaining shape information from a region

[Luis Ibanez]

Hi Aster,

Please gives us a more specific description of the
problem that you are facing.

Are you getting a compilation error ?
if so, please post the error message to the list.

Are you gettting a run time exception ?
if so, please add a try/catch block and post to the
list the error message that you get.

Are you getting an output, but it looks incorrect ?
please gives us a detailed description of
the observations that lead you to think
that the output is incorrect.

The BinaryMask3DMeshSource expects a binary image
as input, and that's what the ConnectedThresholdFilter
produce as output, so you shouldn't have any pipeline
incompatibilities. Please give us more details so we
can track if this issue is a bug in the code.


   Regards,


      Luis


--------------------------------
Aster.Wardhani at csiro.au wrote:
> Thanks for your help & suggestion of using a mesh. I am trying now to
> use the BinaryMask3DMeshSource and trying to input the result from
> connectedThresholdFilter to this object. This does not seem to work to
> directly connecting them in the pipeline. Do I have to somehow convert
> the filter output to a binary image first? I use casting but still not
> working.
> 
> -----Original Message-----
> From: Luis Ibanez [mailto:luis.ibanez at kitware.com] 
> Sent: Wednesday, 24 August 2005 1:33 AM
> To: Wardhani, Aster (ICT Centre, e-Health Res Centre)
> Cc: insight-users at itk.org
> Subject: Re: [Insight-users] Obtaining shape information from a region
> 
> 
> Hi Aster,
> 
> There are filters that will extract the pixels from
> the boundary and set them on in an outptu image:
> 
> SimpleContourExtractorImageFiler
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1SimpleContourExtract
> orImageFilter.html
> 
> You can also use the BinaryMaskToNarrowBandImageFilter
> that will return you a PointSet with all the points
> that are located at a selected distance from the edge
> of your segmented object.
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1BinaryMaskToNarrowBa
> ndPointSetFilter.html
> 
> 
> However, I would strongly discurage you from encoding
> the information of your segmentation in a simple list
> of points, because you will lose all the connectivity
> information, which is very expensive to recover from
> just a cloud of points.
> 
> 
> Of course, it all depends on what is your final goal....
> 
> 
> If you are looking for a Mesh representation of your
> object, then you should consider to include not only
> the points (locations of pixels as returned by the
> IndexToPhysicalPoint() method in the itk::Image), but
> also the neighborhood information.
> 
> 
> You may want to read the "Data Representation" Chapter
> from the ITK Software Guide:
> 
>    http://www.itk.org/ItkSoftwareGuide.pdf
> 
> 
> in order to get familiar with the mechanisms for
> representing Meshes.
> 
> 
> 
>    Regards
> 
> 
> 
>       Luis
> 
> 
> 
> 
> ------------------------------
> Aster.Wardhani at csiro.au wrote:
> 
>>Hi Luis,
>>
>>After I extract a region say using region growing, I'd like to store
> 
> points that belong to the region's boundary and also points that belong
> to the internal region's areas. Does that make sense? Does the filter
> provide a method to return a list of points? Or do I need to do manually
> interate all pixels in the output image then push each pixel as a point
> into a list ?
> 
>>Thanks,
>>
>>Aster.
>>
>>-----Original Message-----
>>From:	Luis Ibanez [mailto:luis.ibanez at kitware.com]
>>Sent:	Tue 8/23/2005 9:09 AM
>>To:	Wardhani, Aster (ICT Centre, e-Health Res Centre)
>>Cc:	insight-users at itk.org
>>Subject:	Re: [Insight-users] Obtaining shape information from a
> 
> region
> 
>>Hi Aster,
>>
>>I'm afraid that you question is too vague in
>>order for us to give you any useful feedback.
>>
>>Shape analysis is a wide field and you should
>>usually start by framing the goal/purpose of
>>your shape analysis task.
>>
>>Maybe a description of the context of your problem
>>would help....
>>
>>
>>   Regards,
>>
>>
>>
>>     Luis
>>
>>
>>-------------------------------
>>Aster.Wardhani at csiro.au wrote:
>>
>>
>>>Hi,
>>>
>>>I've just done some segmentation using connected component filter 
>>>(region grow with a seed point). What's the best way to analyse the 
>>>shape of the region, i.e getting:
>>>
>>>-       its boundary
>>>-       points that belong to the region.
>>>
>>>
>>>----------------------------------------------------------------------
> 
> --
> 
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>>
>>
>>
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>>
> 
> 
>