Richard Beare | 1 Dec 05:01 2005
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how to do tiled subregion operations

Hi,
I'm having problems getting this working. I have a large image created
my mosaicing a number of images together. This is done by some
microscope software. I want to apply some lighting correction to each
sub image. My alternatives seem to be either welding multiple copies
of the background image to create a correction image that is the same
size as the mosaic, break up the mosaic and do the correction on
individual sub regions and the weld together again, or create an
output image of the correct size and type (same as the mosaic),
connect a correction pipeline to the input and correction image and
then reset the RequestedRegion of the output image to each relevant
position, calling Update after each reset. I'm attempting to do this
in python but I'm having trouble connecting the end of the pipeline to
the output image. It is possible that this is because the last
elements in my pipeline are casters of division filters that behave a
bit differently to other filters.

I've also tried some experiments with the RegionOfInterestFilter, without luck.

Is this the right way to go?

Thanks

Incidentally, are there any filters that allow images of the same
dimension to be abutted to create a larger image? I couldn't see
anything.
Ghassan Hamarneh | 1 Dec 06:53 2005
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Re: MeshSpatialObject Issues

On 11/28/05, Julien Jomier <jjomier@...> wrote:
> Hi Chris,
>
> I guess you are trying to use SOViewer to display a 2D mesh (from the
> file you sent). This is currently not possible, therefore only 3D meshes
> are supported (see example at the end of the email). You can try to
> convert your 2D mesh into a 3D one by setting the Z=0 of your points.
>
> Regarding the SpatialObjectToImageFilter, this filter is looking if the
> point is on the mesh (not inside the mesh). That's why (25,25) is
> returning false and currently this function is not implemented for
> LineCells... You can submit a bug report (www.itk.org/Bug) and we'll try
> to implement it.
>
> Let us know if you still have any issues/concerns.
> Thanks,
>
> Julien
>
> ----
> ObjectType = Scene
> NDims = 3
> NObjects = 1
> ObjectType = Mesh
> NDims = 3
> ID = 0
> TransformMatrix = 1 0 0 0 1 0 0 0 1
> Offset = 0 0 0
> CenterOfRotation = 0 0 0
> ElementSpacing = 1 1 1
(Continue reading)

ilker hacıhaliloğlu | 1 Dec 08:22 2005
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Fast marching filter seed points

hi all
 
I want to automatically select the seed points used for FMM level sets. on the mailing list i found somethink related to this.
 
but i have a couple of questions here. First of all is  the labeled image which we are talking here is the segmented result of the confidence connected segmenteation filter?
 
If we are using the labeled image dont we have to first read the image with a reader type? And after  that apply this code?
 
Or the part which is given below is doing the same thing?
 
IteratorType it( image, image->GetBufferedRegion() );
 
 
Cheers
ilker
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Nicolas Forster | 1 Dec 08:28 2005
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MRFImageFilter

Hi, i just have a question about the MRFImageFilter:

On which article or technical report is based the DoNeighborhoodOperation()

thanks Nico
charfeddine amir | 1 Dec 12:41 2005
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about installing ITK VTK FLTK RPMS?

hello world !
i'm new user using linux Mandriva 2006
i've started installing rpm from http://www.creatis.insa-lyon.fr/%7Ebellet/creatis/dogme5/RPMS/

cmake-2.0.5-2.i386.rpm*,  cmake-debuginfo-2.0.5-2.i386.rpm*
fltk-1.1.6-2.i386.rpm*, fltk-debuginfo-1.1.6-2.i386.rpm*, fltk-devel-1.1.6-2.i386.rpm*
gdcm-1.0.1-1.20050504.i386.rpm*, gdcm-debuginfo-1.0.1-1.20050504.i386.rpm*
insightapplications-2.0.1-1.i386.rpm*, insightapplications-debuginfo-2.0.1-1.i386.rpm*

itk-2.0.1-3.i386.rpm*, itk-debuginfo-2.0.1-3.i386.rpm*, itk-devel-2.0.1-3.i386.rpm*, itk-examples-2.0.1-3.i386.rpm*, itk-java-2.0.1-3.i386.rpm*, itk-python-2.0.1-3.i386.rpm*
itk-tcl-2.0.1-3.i386.rpm*, itk-testing-progs-2.0.1-3.i386.rpm*

vtk-4.5.0-1.cvs20040114.i386.rpm*, vtk-data-4.5.0-1.cvs20040114.i386.rpm*, vtk-debuginfo-4.5.0-1.cvs20040114.i386.rpm*, vtk-devel-4.5.0-1.cvs20040114.i386.rpm*, vtk-examples-4.5.0-1.cvs20040114.i386.rpm*, vtk-java-4.5.0-1.cvs20040114.i386.rpm*
vtk-python-4.5.0-1.cvs20040114.i386.rpm*, vtk-qt-4.5.0-1.cvs20040114.i386.rpm*
vtk-tcl-4.5.0-1.cvs20040114.i386.rpm*, vtk-testing-progs-4.5.0-1.cvs20040114.i386.rpm*

the installation was OK but i didn't know what to do after that
is there another step(s) to do before i start programming ( for example using CMAKE)
thankx !

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Renaud Isabelle | 1 Dec 16:14 2005
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Re: how to take into account of pixel size in saving image

Hi,
 
I read the chapter about image formats in the software guide. However, it doesn't say what image format are taking into account the pixel size. i tried with BMP,PNG,JPEG, no one is working!!.
 
ISabelle

Gaetan Lehmann <gaetan.lehmann-XgXWy3RkuaMhT4uAktR2oQ@public.gmane.org> a écrit :

Hi Isabelle,

You should try to resample your image with the resample image filters or use
an image format which store spacing.
There is a chapter about that in the insight software guide.

Regards,

Gaetan


On Wednesday 30 November 2005 23:04, Renaud Isabelle wrote:
> Hi,
>
> I have to save an image of 55*239 pixels with spacing as 0.1496*0.01925.
>
> This seems to be easy. However, the image saved is not taking into
> account my pixel size but just the number of my pixels.
>
> ImageType::IndexType start;
> start.Fill(0);
>
> ImageType::SizeType sz;
> sz[0] = 239;
> sz[1] = 55;
>
> ImageType::RegionType region;
> region.SetSize( sz );
> region.SetIndex( start );
>
> ImageType::Pointer shifty = ImageType::New();
> shifty->SetRegions( region );
> shifty->Allocate();
>
> ImageType::SpacingType spacing ;
> spacing[0] = 0.01925;
> spacing[1] = 0.1496;
> shifty->SetSpacing( spacing );
>
> //compute shifty somehow
>
> typedef itk::RescaleIntensityImageFilter<
> ImageType, WriteImageType > RescaleFilterType;
>
> RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
> rescaler->SetOutputMinimum( 0 );
> rescaler->SetOutputMaximum( 255 );
> rescaler->SetInput( shifty );
>
> typedef itk::ImageFileWriter< WriteImageType > WriterType;
> WriterType::Pointer writer = WriterType::New();
> writer->SetFileName("shifty.jpg");
> writer->SetInput( rescaler->GetOutput() );
> writer->Update();
>
> By taking into account the pixel size, the saved image should be almost
> twice heigher than large. However, taking into account only the number of
> pixels, my saved image is 4 times larger than heigh.
>
> This is a medical image so my pixel size is very important to be aware of
> the physical dimensions of the image.
>
> Isabelle
>
>
>
>
> ---------------------------------
> Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger
> Téléchargez le ici !

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Sylvain Jaume | 1 Dec 16:19 2005

Re: how to take into account of pixel size in saving image

Hi Isabelle,

Have you tried Meta image format?

Best,
Sylvain

Renaud Isabelle wrote:

> Hi,
>  
> I read the chapter about image formats in the software guide. However, 
> it doesn't say what image format are taking into account the pixel 
> size. i tried with BMP,PNG,JPEG, no one is working!!.
>  
> ISabelle
>
> */Gaetan Lehmann <gaetan.lehmann@...>/* a écrit :
>
>
>     Hi Isabelle,
>
>     You should try to resample your image with the resample image
>     filters or use
>     an image format which store spacing.
>     There is a chapter about that in the insight software guide.
>
>     Regards,
>
>     Gaetan
>
>
>     On Wednesday 30 November 2005 23:04, Renaud Isabelle wrote:
>     > Hi,
>     >
>     > I have to save an image of 55*239 pixels with spacing as
>     0.1496*0.01925.
>     >
>     > This seems to be easy. However, the image saved is not taking into
>     > account my pixel size but just the number of my pixels.
>     >
>     > ImageType::IndexType start;
>     > start.Fill(0);
>     >
>     > ImageType::SizeType sz;
>     > sz[0] = 239;
>     > sz[1] = 55;
>     >
>     > ImageType::RegionType region;
>     > region.SetSize( sz );
>     > region.SetIndex( start );
>     >
>     > ImageType::Pointer shifty = ImageType::New();
>     > shifty->SetRegions( region );
>     > shifty->Allocate();
>     >
>     > ImageType::SpacingType spacing ;
>     > spacing[0] = 0.01925;
>     > spacing[1] = 0.1496;
>     > shifty->SetSpacing( spacing );
>     >
>     > //compute shifty somehow
>     >
>     > typedef itk::RescaleIntensityImageFilter<
>     > ImageType, WriteImageType > RescaleFilterType;
>     >
>     > RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
>     > rescaler->SetOutputMinimum( 0 );
>     > rescaler->SetOutputMaximum( 255 );
>     > rescaler->SetInput( shifty );
>     >
>     > typedef itk::ImageFileWriter< WriteImageType > WriterType;
>     > WriterType::Pointer writer = WriterType::New();
>     > writer->SetFileName("shifty.jpg");
>     > writer->SetInput( rescaler->GetOutput() );
>     > writer->Update();
>     >
>     > By taking into account the pixel size, the saved image should be
>     almost
>     > twice heigher than large. However, taking into account only the
>     number of
>     > pixels, my saved image is 4 times larger than heigh.
>     >
>     > This is a medical image so my pixel size is very important to be
>     aware of
>     > the physical dimensions of the image.
>     >
>     > Isabelle
>     >
>     >
>     >
>     >
>     > ---------------------------------
>     > Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo!
>     Messenger
>     > Téléchargez le ici !
>
>
> ------------------------------------------------------------------------
> *Appel audio GRATUIT partout dans le monde* avec le nouveau Yahoo! 
> Messenger
> Téléchargez le ici ! 
> <http://us.rd.yahoo.com/messenger/mail_taglines/default/*http://fr.messenger.yahoo.com> 
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Insight-users mailing list
>Insight-users@...
>http://www.itk.org/mailman/listinfo/insight-users
>  
>
Luis Ibanez | 1 Dec 16:23 2005

Re: how to take into account of pixel size in saving image


Hi Isabelle,

          You are using JPEG as file format.

       Please don't use JPEG for Medical Images.

               It is not good for you,
        and it is not good for the patients

JPEG was designed for compressing images of natural scenes,
such as birthday parties, the picture of a horse, the picture
of a dog sleeping in a backyard, landscape pictures or the photo
of a clown with a pointy hat. The compression dictionary used by
JPEG was fine tunned for the spatial frequencies that appear
commonly in natural scenes. It was not designed for CT scans,
or MRI images, or UltraSounds.

          http://www.faqs.org/faqs/jpeg-faq/part1/

Quote:

> JPEG is designed for compressing either full-color or gray-scale images
> of natural, real-world scenes.  It works well on photographs, naturalistic
> artwork, and similar material; not so well on lettering, simple cartoons,
> or line drawings.  

If you want to manage medical images in a safely way
(and I'm sure you do want to manage them in a safe way)
you should use image file format that are intended for
medical images.

Among the many good choices that you have with ITK,
you could consider the following:

     1) Analyze
     2) MetaImages
     3) GIPL
     4) DICOM

When viewing those images, please use also viewers that
are designed for medical images. Such viewers should take
into account the pixel size of the image.

You could consider the following options:

     1) ImageViewer (in InsightApplications)
     2) Slicer    www.slicer.org
     3) ParaView  www.paraview.org
     4) VolView   www.volview.com

Don't use viewers such as Paint in Windows, or the FaxViewer
(which of course is only intended for Faxes, not for CT scans),
don't use either ImageMagick display. Those naive viewers are
not intended for medical application. They will display images
up-side-down, and will not take into account any pixel size.

Please reserve JPEG for the pictures of family reunions
and vacation trips.

   Regards,

     Luis

-----------------------
Renaud Isabelle wrote:
> Hi,
>  
> I have to save an image of 55*239 pixels with spacing as 0.1496*0.01925.
>  
> This seems to be easy. However, the image saved is not taking into 
> account my pixel size but just the number of my pixels.
>  
> */ImageType::IndexType start;/*
> */start.Fill(0); /*
> *//* 
> */ImageType::SizeType sz;/*
> */sz[0] = 239; /*
> */sz[1] = 55;/*
> *//* 
> */ImageType::RegionType region;/*
> */region.SetSize( sz );/*
> */region.SetIndex( start );/*
> *//* 
> */ImageType::Po! inter shifty = ImageType::New();/*
> */shifty->SetRegions( region );/*
> */shifty->Allocate();/*
> *//* 
> */ImageType::SpacingType spacing ; /*
> */spacing[0] = 0.01925; /*
> */spacing[1] = 0.1496;/*
> */shifty->SetSpacing( spacing );/*
> *//* 
> *///compute shifty somehow/*
> *//* 
> */typedef itk::RescaleIntensityImageFilter</*
> */ImageType, WriteImageType > RescaleFilterType;/*
> *//* 
> */RescaleFilterType::Pointer rescaler = RescaleFilterType::New();/*
> */rescaler->SetOutputMinimum( 0 );/*
> */rescaler->SetOutputMaximum( 255 );/*
> */rescaler->SetInput( shifty );/*
> *//* 
> */typedef itk::ImageFileWriter< WriteImageType > WriterType;/*
> */WriterType::Pointer writer = WriterType::New();/*
> */writer->SetFileName("shifty.jpg");/*
> */writer->SetInput( rescaler->GetOutput() );/*
> */writer->Update();/*
> *//* 
> By taking into account the pixel size, the saved image should be almost 
> twice heigher than large. However, taking into account only the number 
> of pixels, my saved image is 4 times larger than heigh.
>  
> This is a medical image so my ! pixel size is very important to be aware 
> of the physical dimensions of the image.
>  
> Isabelle
>  
> 
> ------------------------------------------------------------------------
> *Appel audio GRATUIT partout dans le monde* avec le nouveau Yahoo! Messenger
> Téléchargez le ici ! 
> <http://us.rd.yahoo.com/messenger/mail_taglines/default/*http://fr.messenger.yahoo.com> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users@...
> http://www.itk.org/mailman/listinfo/insight-users
Luis Ibanez | 1 Dec 16:34 2005

Re: kitware search page problem


Hi Ilker,

     Why would you search the Web with
     anything different than Google ?

         "Resistance is futile"

There is nothing wrong with the Search option
at Kitware.com. It simply seems that you used
the first field in

     http://www.kitware.com/search.html

The first field only visits Kitware's corporate pages.

Please use the second field, where you can search
the public pages for VTK, ITK, CMake.

If you type:

     "shape detection level sets"

in the second search field you will get many hits
from the ITK mailing list.

A much better way of searching for information is to
use the Advanced search page from Google

    http://www.google.com/advanced_search?hl=en

Select the domain to be limited to "www.itk.org"
and type "shape detection level sets" in the search
field.

            That will return you

         155 link from www.itk.org
             in 0.11 seconds.

At that point you will realize why is that only
the Journals that are searchable by Google have
any chances of survival. Closed publications that
do not provide Open Access will become extinct as
part of the natural selection process of the Web.

    Regards,

      Luis

---------------------------
ilker hacıhaliloğlu wrote:
> Hi All
>  
> I was using the http://www.kitware.com/search.html site for searching 
> .But today I encounter some problems?
> For example if i try to search for shape detection level sets I can not 
> get any results. Is there a problem today in this website?
>  
> Cheers
> ilker
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users@...
> http://www.itk.org/mailman/listinfo/insight-users
Luis Ibanez | 1 Dec 16:45 2005

Re: register two volumes of different types

Hi Grace,

                  Yes,

     ITK can register pairs of images
     that have different number of slices.

        or for that matter,
        different number of pixels
        along any dimension.

If your registration program is not working
as you expected, here are the first things
that you should try:

1) Verify the values of Origin and Pixel
    Spacing for both images. Make sure that
    they are realistic values.

2) Use a CenteredTransform Initializer.

3) Connect an Observer to the Optimizer

4) Plot the values of the Metric, at every
    iteration of the optimizer.

5) Plot the list of Transform parameters
    at every iteration of the optimizer

Details on how to do each one of those steps
are presented in the ITK Software Guide

   http://www.itk.org/ItkSoftwareGuide.pdf

If you still have difficulties with your
registration process, please post your problem
as an article to the Insight Journal, and make
sure that you upload your two images, the source
code that you are using, and the parameters that
you  are passing to all the components of the
registration framework.

Please let us know if you have any question on
how to submit a report of negative results.
This is a forgotten art in the practice of scientific
research, mostly due to the detrimental influence of
the decadent publishing system that have provided
Pavlovian training to our community in order to only
report successful experiencies.

   Regards,

     Luis

------------------
Grace Chen wrote:
> Hi there,  Good day!
>  
> I have two 3D image data I want to register.  The movement in the data 
> is 3D rigid.  So, I use VersorRigid3DTransform.  The two volumes are 
> different types of image data (one is T1 image, and the other 
> is diffusion weighted image), so I use 
> MattesMutualInformationImageToImageMetric. I know ITK can register two 
> volumes of different physical dimension.  But doesn't it also register 
> two volumes that have different number of slices?  My program doesn't 
> work for two volumes of different types, am I missing something?
>  
> Grace 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Insight-users mailing list
> Insight-users@...
> http://www.itk.org/mailman/listinfo/insight-users

Gmane