[Insight-users] watershed with MRI

[Joshua Cates]

Hi,

Yes, the test is perhaps misleading as it doesn't really produce any
meaningful output, just excercises the code.  The filters are fine, the
data is just not interesting and only segments to one region at most level
values.  At some point I will replace the test with one using actual image
data that will produce more meaningful results for true regression
testing.

I suggest looking at the example in the Applications directory instead
(Applications/WatershedSegmentation).  This example is more instructive as
it shows how to preprocess the data and produce output at different
levels.  It will read images in ASCII pgm format.

Also, the extremely high value you are seeing looks like the result 
of the wrong endianness.

Josh.

______________________________
 Josh Cates			
 School of Computer Science	
 University of Utah
 Email: cates@sci.utah.edu
 Phone: (801) 587-7697
 URL:   http://www.sci.utah.edu/~cates


On Wed, 8 Jan 2003, lydia coin wrote:

> 
> Hi Josh,
> I changed the value of the level paramter from 1 to 0.1 and to 0.01, but still the same intensity value of 3452816845 for the whole image. it's really strange, I wonder if this example in the testing folder gives the same result for you
>  Joshua Cates <cates@sci.utah.edu> wrote:Hi Lydia,
> 
> For your MRI image, make sure that you cast to float (or double) before 
> passing to the GradientMagnitudeImageFilter. You might also want to do 
> some smoothing on the image first (i.e. 
> Gradient/CurvatureAnisotropicDiffusionImageFilter or 
> BilateralImageFilter). 
> 
> In your example code below, you set the Level parameter to 1.0. This 
> should result in an output of exactly one region because it is telling the 
> filter to merge all of the potential watershed basins up to 100% of the 
> possible image height. Try a Level parameter much lower than this, say 
> 0.10 (i.e. 10% of the height).
> 
> Josh.
> 
> ______________________________
> Josh Cates 
> School of Computer Science 
> University of Utah
> Email: cates@sci.utah.edu
> Phone: (801) 587-7697
> URL: http://www.sci.utah.edu/~cates
> 
> 
> On Wed, 8 Jan 2003, lydia coin wrote:
> 
> > 
> > thank you for your hints.
> > 
> > That what I did, I used an MRI image, with the GradientMagnitudeImageFilter and pass it to the watershed filter. the result is an image with the same intensity value.
> > 
> > In addition to using MRI image, I took the image of the testing example as follows (source code below). The result is an image with the same intensity value everywhere in the image ( like for the MRI). In this case the pixel type is float but still doesn't work. I'll cast the MR image to float but in the meanwhile, could you have a look to my code, maybe something is wrong. 
> > 
> > 
> > 
> > typedef itk::Image ImageType2D;
> > itk::ImageRegion<2> Region2D;
> > itk::Size<2> size2D;
> > size2D[0] = 256;
> > size2D[1] = 256;
> > itk::Index<2> orig2D;
> > orig2D[0] = 0;
> > orig2D[1] = 0;
> > 
> > Region2D.SetSize(size2D);
> > Region2D.SetIndex(orig2D);
> > 
> > ImageType2D::Pointer image2D = ImageType2D::New();
> > image2D->SetLargestPossibleRegion(Region2D);
> > image2D->SetBufferedRegion(Region2D);
> > image2D->SetRequestedRegion(Region2D);
> > image2D->Allocate();
> > 
> > 
> > itk::ImageRegionIterator
> > it2D(image2D, image2D->GetRequestedRegion()); 
> > 
> > float q = 0.00f;
> > for (; !it2D.IsAtEnd(); ++it2D)
> > {
> > it2D.Value() = ::sin(q);
> > q = q + 0.10f;
> > }
> > 
> > float lower_threshold=.05f;
> > itk::WatershedImageFilter::Pointer watershed
> > = itk::WatershedImageFilter::New();
> > watershed->SetThreshold(lower_threshold);
> > watershed->SetLevel(1.0f);
> > watershed->SetInput(image2D);
> > typedef unsigned long PixelType1;
> > PixelType1 *data = new PixelType1[size[0]*size[1]];
> > typedef itk::ImageRegionIteratorImageIterator1;
> > ImageIterator1 it1(watershed->GetOutput(),watershed->GetOutput()->GetBufferedRegion());
> > it1.GoToBegin();
> > int i=0;
> > while( !it1.IsAtEnd() )
> > {
> > data[i]=it1.Get( );
> > ++it1;
> > i++;
> > }
> > 
> > 
> > 
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