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

Wed Feb 24 00:34:38 EST 2016

Thanks Dženan.

It worked after I set origin to (0,0).

Regards,
Gunjan Naik

Gunjan G. Naik | Persistent LABS | PhD Student – University of Pune
gunjan_naik at persistent.com<mailto:gunjan_naik at persistent.com> | Cell: +91-8087996979 | 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 16, 2016 8:46 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,

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<mailto: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<mailto:gunjan_naik at persistent.com> | Cell: +91-8087996979<tel:%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<mailto:dzenanz at gmail.com>]
Sent: Tuesday, February 09, 2016 8:53 PM
To: Gunjan Naik <gunjan_naik at persistent.com<mailto:gunjan_naik at persistent.com>>
Cc: insight-users at itk.org<mailto: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<mailto: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<mailto:gunjan_naik at persistent.com> | Cell: +91-8087996979<tel:%2B91-8087996979> | Tel: +91-20-670 34878
Persistent Systems Ltd. | Partners in Innovation | www.persistent.com<http://www.persistent.com/>

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