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

Gunjan Naik gunjan_naik at persistent.com
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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DISCLAIMER
==========
This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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