[Insight-users] Skeleton - itkBinaryThinningImageFilter3D

[Daniela Sacchetto]

Sergio, thanks for your clarification.

 I use ImageJ and, following your advise, I change the "Enhance Contrast" options, setting them to "Normalize"... now I can see the skeleton!

Regards
Daniela

Date: Mon, 31 May 2010 10:01:00 +0200
Subject: Re: [Insight-users] Skeleton - itkBinaryThinningImageFilter3D
From: sergio.vera at alma3d.com
To: danysunflower at hotmail.it
CC: luis.ibanez at kitware.com; insight-users at itk.org

Hello

My guess is that the output image is correct, but your visualization software has incorrect window/level values so you cannot see the white (255) pixels.

Use your software window/level options and try to adjust them until you see the skeleton or use another tool to generate an isosurface from the skeleton.

I often use Seg3D to visualize data because it does not mess with window/level stuff and also does not shown interpolated images so what I see is closer to what the image really is.

regards



On Sat, May 29, 2010 at 6:05 PM, Daniela Sacchetto <danysunflower at hotmail.it> wrote:






Hi Luis,
your mails are always very useful for my works...

I did what you asked me and thi is the output:

OUTok.dcm sucessfully read.

imageMin: 255
imageMax: 0

Skpr.dcm sucessfully written.

Program terminated normally.

What does it mean? It looks that some pixel are not black.....

Regards,
Daniela


Date: Sat, 29 May 2010 11:05:58 -0400
Subject: Re: [Insight-users] Skeleton - itkBinaryThinningImageFilter3D

From: luis.ibanez at kitware.com
To: danysunflower at hotmail.it
CC: dan.muel at gmail.com; insight-users at itk.org



Hi Daniela,

First you have to verify if the output of the skeletonization
filter had indeed all its pixels set to zero.

You can do this with code similar to


  #include "itkMinimumMaximumImageFilter.h"

  typedef 
    itk::MinimumMaximumImageFilter<ScalarImageType> MinMaxFilterType;

   MinMaxFilterType::Pointer minmaxFilter   = MinMaxFilterType::New();

   skeletonFilter->Update();

   image = skeletonFilter->GetOutput();


   imageMin  = minmaxFilter->GetMinimum();
   imageMax = minmaxFilter->GetMaximum();


   and printing out these values.

   In this way, you will remove the confounding factors of

    * Saving the image in DICOM, and


    * The visualization program / method that you use.



    Please let us know what you find,

         Thanks


              Luis


-----------------------------------------------------------------------------------


On Sat, May 29, 2010 at 10:39 AM, Daniela Sacchetto <danysunflower at hotmail.it> wrote:







Thanks for your clarification, now I can compile my code in Release Mode and I have my output in a few seconds.

Neverthless now I have an other problem that I want to discuss with you. 

My output is an dcm image but its pixels are all black...I can't see the skeleton because in my image all the white pixel disappear.... I think that it is a problem of algorithm's setting and that it erodes too much my image but I don't know how to solve this problem...


Could anyone help me?

Thanks a lot
Daniela


 		 	   		  
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