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

[Matt McCormick]

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.
>>>
>>
>>
>
>
>
>