[Insight-users] Extraction of mandible

[Luis Ibanez]

Hi Ali,

               ITK manages N-Dimensional images.

It is better to perform the segmentation in the 3D image itself.

Working with individual 2D slices bring many unnecessary
complications to the segmentation process. You can avoid
them by working directly in 3D.


Simply instantiate the region growing filter by using a 3D
image type.


See for example:

    InsightApplications/Auxiliary/vtk
           itkReadITKImage3DSegmentShowVTK.cxx

http://public.kitware.com/cgi-bin/viewcvs.cgi/Auxiliary
/vtk/itkReadITKImage3DSegmentShowVTK.cxx?revision=1.11&root=InsightApplications&view=markup


In particular,
please note that the seed point must be provided
by the user. Here we use the primitive method:

    if( argc >  4 )
      {
      seed[0] = atoi( argv[2] );
      seed[1] = atoi( argv[3] );
      seed[2] = atoi( argv[4] );
      }

    filter->SetSeed( seed );


but, using a VTK picker or a vtkPointWidget
will provide a more elegant way of gathering
the seed point from the user.


     Regards,


             Luis


-----------------------------------------------------------------------------------
On Sun, Mar 7, 2010 at 4:12 AM, Ali Habib <ali.mahmoud.habib at gmail.com> wrote:
> Dear Kuis,
>
> thanks for reply, I have small question,
> I read DICOM series and reconstruct it to get the 3D skull, select the
> point in mandible  at the level of 3D reconstructed or at teh level of the
> 2D series
>
> sorry for myquestions, but I'm new to VTK, ITK and segmentation
>
> Best regards
> On Sun, Mar 7, 2010 at 2:19 AM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>
>> Hi Ali,
>>
>> Thanks for posting your code.
>>
>> The likely source of the problem is that
>> you are currently setting the seed point
>> in the middle of the image:
>>
>>       seed[0] = start[0] + size[0] / 2;
>>       seed[1] = start[1] + size[1] / 2;
>>       seed[2] = start[2] + size[2] / 2;
>>
>>
>> The seed point should be placed inside
>> the mandibule (or any other anatomical
>> structure that you want to segment).
>>
>> Typically, a seed point is placed interactively
>> by offering a GUI+Visualization to the user.
>>
>> There are multiple ways in VTK to get the
>> coordinates of a pixel in which the user has
>> clicked (for example the vtkWorldPointPicker)
>>
>> You may also want to start with a smaller value
>> for the sigma multiplier (e.g. 1.5 instead of 2.5),
>> and only increase that value if your segmentation
>> doesn't include the entire mandible.
>>
>> You may want to read the description of this
>> region growing segmentation filter in the
>> ITK Software Guide:
>>
>>  http://www.itk.org/ItkSoftwareGuide.pdf
>>
>>
>>
>>     Regards,
>>
>>
>>            Luis
>>
>>
>>
>> ------------------------------------------------------------------------------------------------------
>> On Fri, Mar 5, 2010 at 6:03 PM, Ali Habib <ali.mahmoud.habib at gmail.com>
>> wrote:
>> > Dear Luis,
>> > I tried to use confidenceconnected filter, and watersheed filter but
>> > displaying the output is white
>> > I attached the confidence code I use , please help me in it
>> > Best regards
>> >
>> > On Tue, Feb 16, 2010 at 12:51 AM, Luis Ibanez <luis.ibanez at kitware.com>
>> > wrote:
>> >>
>> >> Hi Ali,
>> >>
>> >> What image modality do you have ?
>> >>
>> >> Do you have a CT scan ?
>> >>
>> >>
>> >> If so,
>> >> you may want to experiment with the following filters:
>> >>
>> >>
>> >>    1) ConfidenceConnectedImageFilter, or
>> >>    2) IsolatedConnectedImageFilter
>> >>
>> >>
>> >> You will find them described in the ITK Software Guide
>> >>
>> >>    http://www.itk.org/ItkSoftwareGuide.pdf
>> >>
>> >>
>> >> and you will find source code examples in
>> >>
>> >>           Insight/Examples/Segmentation
>> >>
>> >>
>> >>   Regards,
>> >>
>> >>
>> >>      Luis
>> >>
>> >>
>> >> ------------------------------------------------------------------
>> >> On Mon, Feb 15, 2010 at 8:43 AM, Ali Habib
>> >> <ali.mahmoud.habib at gmail.com>
>> >> wrote:
>> >> > Dear All,
>> >> >
>> >> >
>> >> > I need to segemnt 3D reconstruction of skull,  do any one have any
>> >> > idea
>> >> > resource for doing that
>> >> >
>> >> > Best regards
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>> >
>
>