[ITK-users] [ITK] help- find position of seed-levelset segmentation/connected treshold

[Sindhoor Bhat]

Hi Nicolas, Matt,

Finally I found out what the problem was.
I had to : SetInput (roi_filter->GetOutput() ) to the Fast marching filter , other than specifying :  fastMarching->SetOutputSize( rescaleFilter->GetOutput()->GetBufferedRegion().GetSize() );

below link helped me :
http://www.itk.org/pipermail/insight-users/2010-May/036993.html


I think in ITK manual : this is given in words like : Note that the size is obtained here from
the output image of the smoothing filter. The size of this image is valid only after the Update()
methods of this filter have been called directly or indirectly........ page 503

anyway thanks for your help :)



On Wednesday, 18 June 2014 11:29 AM, Sindhoor Bhat <bhatsindhoor at ymail.com> wrote:
 


Hi Matt,
Here is the error. 
vtkImageImport (0000000002750400): Calling UpdateInformationCallback: c:\itk file\source\modules\core\common\include\itkImageToImageFilter.hxx:248:


When I checked a lot on itk forums, it was mentioned that this problem is due to some ITK version update .
Really dont know what the problem is,
I removed ROI filter etc but still problem exists
can you pls tell what the problem is.


On Tuesday, 17 June 2014 7:38 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
 


Hi Sindhoor,

Look at image->GetLargestPossibleRegion() to reveal if that is a valid
index inside the image.

Make sure the Image Origin and Spacing are as expected.

The ITK Software Guide [1] has a good explanation on the relationship
between index space and physical space.

Hope this helps,
Matt

[1] http://itk.org/ItkSoftwareGuide.pdf


On Mon, Jun 9, 2014 at 11:51 AM, Sindhoor Bhat <bhatsindhoor at ymail.com> wrote:
> Hi Matt /ITK
>
> Using TransformPhysicalPointToIndex I was able to get pixel index.
> But in Z direction I've got negative value 44, 61, -157
>
> I want to use this point as seed. But When I use this am getting black
> screen as output.
>
> Is it ok
 to use -ve Z or should I do changes?
>
> Also image index is not at the bottom left corner as mentioned in ITK
> manual. it is somewhere near mid bottom end
>
> Can you pls give some light on this?
> thanks
>
>
>
>
>
>
>
> On Sunday, 8 June 2014 8:34 AM, Sindhoor Bhat <bhatsindhoor at ymail.com>
> wrote:
>
>
> thanks Matt. Will try this.
>
>
> On Sunday, 8 June 2014 1:09 AM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>
>
> Hi Sindoor,
>
> itk::Image contains methods like TransformPhysicalPointToIndex [1]
> that can be helpful.
>
> Matt
>
> [1]
> http://www.itk.org/Doxygen/html/classitk_1_1ImageBase.html#af4a7c9c3787e9fdafbaaade2e02efa25
>
> On Sat, Jun 7, 2014 at 7:09 AM, Sindhoor Bhat <bhatsindhoor at ymail.com>
> wrote:
>> Dear Matt/itk users,
>> Now I'm able to pick world coordinates using vtk point picker widget.
>> But for seed input to itk, we need index.  I'm really struck. can you
 pls
>> help me how to move further? using itk-vtk interaction for seed selection?
>>
>> Also, to call vtk window for point selection which command should i use?
>> (is
>> it call-back function in vtk? But from itk how to call ?)
>>
>> thank you
>>
>>
>> On Friday, 6 June 2014 6:04 PM, Matt McCormick
>> <matt.mccormick at kitware.com>
>> wrote:
>>
>>
>> Hi Sindhoor,
>>
>> In your previous mail, you described taking sub-regions, which changes
>> index positions.  To sample a value from a physical position, use an
>> itk::InterpolateImageFunction.
>>
>> The apparent flip may be due to a difference in the direction and
>> location of the Y-axis in your visualization programs.
>>
>> Hope this helps,
>> Matt
>>
>> On
 Fri, Jun 6, 2014 at 1:03 AM, Sindhoor Bhat <bhatsindhoor at ymail.com>
>> wrote:
>>> Thanks Matt for your suggestion.
>>> *But I've tried with that too. It is not considering the index/seed
>>> position
>>> that I write in program.
>>> When I  added  below code to get selected seed position, it shows
>>> completely different point than what I had written(using image J --->
>>> physical coordinates )
>>>           
     std::cout <<  filter->GetOutput()->GetPixel( Position1 )
>>> <<
>>> std::endl;
>>> *seed point doesn't appear between selected thresholds ( say: (85,300) &
>>> seep position will be like 45 etc)
>>>
>>> *Also, I should mention that my dicom images appear in reverse order(
>>> flipped). Is this affecting my seed selection?
>>>        (I tried subtracting Y coordinate from maxY etc.)
>>>
>>> Can you pls tell what is wrong? thank you.
>>>
>>
>>
>
>
>
>
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