[ITK-users] Issue with Seed points in Geodesic Active contour

[Dženan Zukić]

Hi Naik,

with directions being identity matrix and

Size: [240, 240, 155]
Spacing: [1, 1, 1]
Origin: [0, -239, 0]

the physical extent of your image is x: -0.5 to 239.5, y: -239.5 to 0.5 and
z: -0.5 to 154.5 (all millimeters). In other words, x and z are positive,
while y is negative.

HTH,
Dženan

On Tue, Feb 16, 2016 at 7:40 AM, Gunjan Naik <gunjan_naik at persistent.com>
wrote:

> Hi Dženan
>
>
>
> I am using T1 weighted brain tumor image from BRATS challenge.
>
>
>
> The meta information is as follows:
>
> Image (00000000193D62F0)
>
>   RTTI typeinfo:   class itk::Image<short,3>
>
>   Reference Count: 1
>
>   Modified Time: 1194
>
>   Debug: Off
>
>   Object Name:
>
>   Observers:
>
>     none
>
>   Source: (none)
>
>   Source output name: (none)
>
>   Release Data: Off
>
>   Data Released: False
>
>   Global Release Data: Off
>
>   PipelineMTime: 1034
>
>   UpdateMTime: 1193
>
>   RealTimeStamp: 0 seconds
>
>   LargestPossibleRegion:
>
>     Dimension: 3
>
>     Index: [0, 0, 0]
>
>     Size: [240, 240, 155]
>
>   BufferedRegion:
>
>     Dimension: 3
>
>     Index: [0, 0, 0]
>
>     Size: [240, 240, 155]
>
>   RequestedRegion:
>
>     Dimension: 3
>
>     Index: [0, 0, 0]
>
>     Size: [240, 240, 155]
>
>   Spacing: [1, 1, 1]
>
>   Origin: [0, -239, 0]
>
>   Direction:
>
> 1 0 0
>
> 0 1 0
>
> 0 0 1
>
>
>
>   IndexToPointMatrix:
>
> 1 0 0
>
> 0 1 0
>
> 0 0 1
>
>
>
>   PointToIndexMatrix:
>
> 1 0 0
>
> 0 1 0
>
> 0 0 1
>
>
>
>   Inverse Direction:
>
> 1 0 0
>
> 0 1 0
>
> 0 0 1
>
>
>
>   PixelContainer:
>
>     ImportImageContainer (000000001917BD50)
>
>       RTTI typeinfo:   class itk::ImportImageContainer<unsigned
> __int64,short>
>
>       Reference Count: 1
>
>       Modified Time: 1190
>
>       Debug: Off
>
>       Object Name:
>
>       Observers:
>
>         none
>
>       Pointer: 000000001B8E0040
>
>       Container manages memory: true
>
>       Size: 8928000
>
>       Capacity: 8928000
>
>
>
> I am passing co-ordinate to tumor region using Opencv.
>
>
>
> Thanks and Regards,
>
> Gunjan Naik
>
>
>
> *Gunjan G. Naik **|** Persistent LABS | PhD Student – University of Pune*
>
> *gunjan_naik at persistent.com <gunjan_naik at persistent.com>* *|** Cell:
> +91-8087996979 <%2B91-8087996979> **| **Tel: +91-20-670 34878*
>
> *Persistent Systems Ltd. | **Partners in Innovation **| *
> *www.persistent.com* <http://www.persistent.com/>
>
>
>
> *From:* Dženan Zukić [mailto:dzenanz at gmail.com]
> *Sent:* Tuesday, February 09, 2016 8:53 PM
> *To:* Gunjan Naik <gunjan_naik at persistent.com>
> *Cc:* insight-users at itk.org
> *Subject:* Re: [ITK-users] Issue with Seed points in Geodesic Active
> contour
>
>
>
> Hi Naik,
>
>
>
> you should provide your image's meta-information e.g. by:
>
> std::cout<<theImageInQuestion;
>
> as well as coordinates of the point which you try to pass. Then we will be
> able to tell you what is wrong.
>
>
>
> Regards,
>
> Dženan
>
>
>
> On Tue, Feb 9, 2016 at 1:12 AM, Gunjan Naik <gunjan_naik at persistent.com>
> wrote:
>
> Hi All,
>
>
>
> I am using geodesic active contour for brain tumor segmentation.
>
>
>
> In that, I have to give seed points for creating level set.
>
>
>
> I have calculated seed points using opencv, but when I input these points
> using ‘TransformPhysicalPointToIndex’ it throws error stating that index
> out of bounds.
>
>
>
> It works for only points [(0,0)].
>
>
>
> Please provide me directions.
>
>
>
> Thanks and Regards,
>
> Gunjan Naik
>
>
>
>
>
> *Gunjan G. Naik **|** Persistent LABS | PhD Student – University of Pune*
>
> *gunjan_naik at persistent.com <gunjan_naik at persistent.com>* *|** Cell:
> +91-8087996979 <%2B91-8087996979> **| **Tel: +91-20-670 34878*
>
> *Persistent Systems Ltd. | **Partners in Innovation **| *
> *www.persistent.com* <http://www.persistent.com/>
>
>
>
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