Insight Journal | 1 Dec 2010 04:04

The Insight Journal-New Submission

Hello,
A new submission has been added to the Insight Journal.

Title: Escher's Ants as Metaphor:   Topological Marching for the Well-Composed, Genus Zero Crowd
Author(s):Tustison N., Avants B., Siqueira M., Gee J.
Abstract: 
Topological considerations for segmentation results are important for such applications as proper
brain segmentation from digital image data. We present an enhancement of the FastMarchingImageFilter
which allows for topologically constrained evolution of the level set. Identical to the original
functionality of the FastMarchingImageFilter, the evolution of the level set of a single or multiple
genus zero, well-composed seed objects proceeds according to the specified parameters. With our
proposed enhancements, the user can either choose to prevent the level set from merging with itself such
that the original topology of the initial seed object(s) is not violated or that no handles are created
during the evolution process. However, in contrast to earlier approaches which relied on the conce
 pt of the {em simple point} implicitly requiring the definition of a user-specified
foreground/background connectivity, we use the related, but more restrictive concept of
well-composed set!
 s to topologically constrain the evolution of the level set. Utility of our submission is demonstrated on
both 2-D and 3-D brain images.

Download and Review the paper at: http://www.insight-journal.org/browse/publication/778

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Luis Ibanez | 1 Dec 2010 04:29
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Re: registration using rotation + translation

Hi Kevin

On Tue, Nov 30, 2010 at 1:23 PM, Kevin Neff <kevin.l.neff <at> gmail.com> wrote:
>
> Thanks, Dan.  I used the example ImageRegistration8.cxx with my data.
>
> First, it's terribly slow.  Is there anything I can do to speed it up?

1)  How long it took ?

2)  How many cores do you have ?

3) What version of ITK are you using ?

4) Make sure that you compile it for Release mode.
     (that easily makes a difference of 10x with respect to Debug mode).

> my limited experience, applying a threshold first and skipping rotation of
> voxels below the threshold helped.  Or could I pre-compute isotropic voxels
> and skip the interpolation that follows image rotation and just interpolate
> the final solution?  Any suggestion is welcome!
>

You could also use a Mask,
See example:

ITK/Examples/Registration/ImageRegistration12.cxx

> Second, after 200 iterations,  the output does not appear correct.  I ran it
> with data that had the dimensions 13888x560x48 and 1388x560x53 but the
(Continue reading)

Luis Ibanez | 1 Dec 2010 04:30
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Re: Registration for set of medical images

H-B,

It depends...

1) What is the content of your images ?

2) Do you have multiple modalities ?

3) What kind of segmentation are you planning to do ?


    Luis


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

On Sun, Nov 28, 2010 at 11:19 AM, H-B <h4cd-/E1597aS9LQAvxtiuMwx3w@public.gmane.org> wrote:
Hello,
 
 
i want to segment objects from set of images (png or dcom).
 
is the registration important as a preprocees for images? or it wouldn't affect?
 
 
Regards
 
  H.B


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Luis Ibanez | 1 Dec 2010 04:37
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Re: Asking open sourse!!!

Hi Adam,

Instructions on how to download ITK are here:

   http://itk.org/ITK/resources/software.html

Please let us know if you find any problems,

Once you download the Tar or .zip files
and expand them, you will find the registration
examples in the directory

          ITK/Examples/Registration

You can also download the code from our Git
repository:

   http://www.itk.org/Wiki/ITK/Git/Download

In which case, you probably want to get the
release branch.

    Regards,

        Luis

------------------------------------------------
2010/11/26 Adam YEO <hihiuj <at> hotmail.com>:
> Dear, all
>
> I am a 'pure beginnger' who try to use IGS toolkit for a deformable image
> registration work.
>
> Reading the manual, there is a statement that " The source code for this
> section can be found in the file
> Examples/Registration/DeformableRegistration2.cxx."
>
> However, I can not find any other 'Registration' file in the Example folder!
>
> Please let me know if a really generous somebody has the open sourse for the
> DeformableRegistration or Demons-Deformable Registration.
>
> Best wishes,
>
> Adam
>
> _____________________________________
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>
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>
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Luis Ibanez | 1 Dec 2010 04:39
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Re: CUDA code?

Dženan

You may find this project interesting:

      http://sourceforge.net/projects/cudaitk/

Also, as Dan pointed out, as part of the ITKv4 effort,
support for GPU processing will be added to ITK.

We are still evaluating if such implementation should
be made with CUDA or with OpenCL.

     Regards,

         Luis

----------------------------------
2010/11/26 Dan Mueller <dan.muel <at> gmail.com>:
> Hi Dženan,
>
> From my understanding GPU acceleration is a ITKv4 topic:
>   http://www.itk.org/Wiki/ITK_Release_4/GPU_Acceleration
>
> I'm not sure of the progress to date...
>
> Cheers, Dan
>
> 2010/11/26 Dženan Zukić <dzenanz <at> gmail.com>:
>> Hi everyone,
>> this week I started converting some of my computation-intensive code from
>> C++ to CUDA. However, it appears right now that I will have to write some of
>> the ITK filters in CUDA myself (namely
>> itkGradientRecursiveGaussianImageFilter and GradientToMagnitudeImageFilter),
>> or simply execute those filters on CPU and pass the results to CUDA code.
>> Does anyone have CUDA implementation of those filters? Or some other related
>> suggestions?
>> Regards,
>> Dženan
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Luis Ibanez | 1 Dec 2010 04:45
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Re: information about Cuda and ITK image registration

Hi Monica

You may want to follow the initiative for
adding GPU support to ITKv4:
http://www.itk.org/Wiki/ITK_Release_4/GPU_Acceleration

You may also want to take a look at:
http://sourceforge.net/projects/cudaitk/

or
http://code.google.com/p/cuda-insight-toolkit/

   Regards,

        Luis

---------------------------------
On Tue, Nov 23, 2010 at 9:52 AM, Monica Hernandez Gimenez
<mhg@...> wrote:
> Dear ITK users,
>
> I am interested in parallelization of image registration algorithms with
> Cuda.
> I found this project in Namic web page,
>
> http://www.na-mic.org/Wiki/index.php/ITK_Image_Registration_with_CUDA
>
> however, I could not find any further information.
>
> Could somebody tell me what is the status of this project at present (or
> any similar
> existing projects I am not aware of)? Are there already available any
> source codes
> to start with or should I start from scratch?
>
> Thanks a lot!!
>
> Monica.
> _____________________________________
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>
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Luis Ibanez | 1 Dec 2010 04:47
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Re: Streaming Writer Broken?

Hi Kevin,

What version of ITK are you using for this test ?

Please let us know,

    Thanks

         Luis

------------------------------
On Fri, Nov 19, 2010 at 1:00 PM, Kevin H. Hobbs <hobbsk <at> ohiou.edu> wrote:
> I'm trying to stream the full Visible Woman Head data, but it looks like
> the something is still trying to allocate too much memory. Without
> ulimit I just get "swap-death"
>
> I run :
>
> ulimit -v 6291456 # I don't want the OS to start swapping.
> ./StreamedVectorGradientMagnitudeImageFilter \
>  ~/bubbles/VisibleWomanHead/RawRGB/VisibleWomanHeadFull.mhd \
>  VisibleWomanHeadFull_GradMag.mhd \
>  100 # The number of streamed pieces
>
> 100 pieces should keep me well below the 6 GiB limit yet :
>
> VectorCastImageFilter 0.99
> VectorCastImageFilter 1
> VectorCastImageFilter 1
>
> itk::MemoryAllocationError (0x7fc34c000ad0)
> Location: "TElement* itk::ImportImageContainer<TElementIdentifier,
> TElement>::AllocateElements(TElementIdentifier) const [with
> TElementIdentifier = long unsigned int, TElement = itk::Vector<float, 3u>]"
> File: /home/kevin/kitware/ITK/Code/Common/itkImportImageContainer.txx
> Line: 191
> Description: Failed to allocate memory for image.
>
> So I tried it again without the 6GiB limit and in one piece :
>
> ./StreamedVectorGradientMagnitudeImageFilter \
>  ~/bubbles/VisibleWomanHead/RawRGB/VisibleWomanHeadFull.mhd \
>  VisibleWomanHeadFull_GradMag.mhd \
>  1
>
> Which just squeaks in under the available 12GB, swaps very little, and
> completes successfully.
>
> With my brand new 1.3GiB scalar image I tried to simply stream read and
> write with no filter.
>
> ./StreamedScalarImageReadWrite \
>  VisibleWomanHeadFull_GradMag.mhd \
>  VisibleWomanHeadFull_GradMag_100.mhd \
>  100 # The number of streamed pieces
>
> I got this weirdness :
>
> ImageFileWriter 0.99
> WARNING: In /home/kevin/kitware/ITK/Code/IO/itkMetaImageIO.cxx, line 1453
> MetaImageIO (0x10a0200): Unsupported metaData item
> ITK_CoordinateOrientation of type
> N3itk18SpatialOrientation31ValidCoordinateOrientationFlagsEfound, won't
> be written to image file
>
> ImageFileWriter 1
> *** glibc detected *** ./StreamedScalarImageReadWrite: corrupted
> double-linked list: 0x00000000010b9d10 ***
>
> There was no swap death or excessive memory usage but the program didn't
> exit and I had to <ctl>-C out.
>
> I tried to stream the RGB data :
>
> ./StreamedRGBImageReadWrite \
>  ~/bubbles/VisibleWomanHead/RawRGB/VisibleWomanHeadFull.mhd \
>  VisibleWomanHeadFull.mhd \
>  100
>
> Which gave me :
>
> ImageFileWriter 0.98
> ImageFileWriter 0.99
> ImageFileWriter 1
> *** glibc detected *** ./StreamedRGBImageReadWrite: double free or
> corruption (!prev): 0x000000000281b710 ***
> ======= Backtrace: =========
> /lib64/libc.so.6[0x3ee5a75676]
> /home/kevin/kitware/ITK_Build/bin/libITKMetaIO.so.4.0(_ZN10MetaObject15ClearUserFieldsEv+0x2d)[0x7fc39c46548d]
> /home/kevin/kitware/ITK_Build/bin/libITKMetaIO.so.4.0(_ZN10MetaObjectD1Ev+0x49)[0x7fc39c4665a9]
> /home/kevin/kitware/ITK_Build/bin/libITKIO.so.4.0(_ZN3itk11MetaImageIOD1Ev+0x22)[0x7fc39fe7fa42]
> /home/kevin/kitware/ITK_Build/bin/libITKIO.so.4.0(_ZN3itk11MetaImageIOD0Ev+0x9)[0x7fc39fe7fa79]
> /home/kevin/kitware/ITK_Build/bin/libITKCommon.so.4.0(_ZNK3itk6Object10UnRegisterEv+0x4e)[0x7fc3a01c1bee]
> ./StreamedRGBImageReadWrite(_ZN3itk12SmartPointerINS_11ImageIOBaseEE10UnRegisterEv+0x35)[0x4280b1]
> ./StreamedRGBImageReadWrite(_ZN3itk12SmartPointerINS_11ImageIOBaseEED1Ev+0x18)[0x4264ac]
> ./StreamedRGBImageReadWrite(_ZN3itk15ImageFileWriterINS_5ImageINS_8RGBPixelIhEELj3EEEED2Ev+0x5f)[0x42d987]
> ./StreamedRGBImageReadWrite(_ZN3itk15ImageFileWriterINS_5ImageINS_8RGBPixelIhEELj3EEEED0Ev+0x18)[0x42da1e]
> /home/kevin/kitware/ITK_Build/bin/libITKCommon.so.4.0(_ZNK3itk6Object10UnRegisterEv+0x4e)[0x7fc3a01c1bee]
> ./StreamedRGBImageReadWrite(_ZN3itk12SmartPointerINS_15ImageFileWriterINS_5ImageINS_8RGBPixelIhEELj3EEEEEE10UnRegisterEv+0x35)[0x4241c1]
> ./StreamedRGBImageReadWrite(_ZN3itk12SmartPointerINS_15ImageFileWriterINS_5ImageINS_8RGBPixelIhEELj3EEEEEED1Ev+0x18)[0x42361c]
> ./StreamedRGBImageReadWrite(main+0x25b)[0x42085f]
> /lib64/libc.so.6(__libc_start_main+0xfd)[0x3ee5a1ec5d]
> ./StreamedRGBImageReadWrite[0x420549]
> ======= Memory map: ========
> 00400000-00455000 r-xp 00000000 fd:00 1835307
>  /home/kevin/Documents/StreamingTest/StreamedRGBImageReadWrite
> 00654000-00655000 rw-p 00054000 fd:00 1835307
>  /home/kevin/Documents/StreamingTest/StreamedRGBImageReadWrite
> 00655000-00656000 rw-p 00000000 00:00 0
> 023e7000-028e1000 rw-p 00000000 00:00 0
>  [heap]
> 3ee5600000-3ee561e000 r-xp 00000000 fd:01 12959
>  /lib64/ld-2.12.1.so
> 3ee581d000-3ee581e000 r--p 0001d000 fd:01 12959
>  /lib64/ld-2.12.1.so
> 3ee581e000-3ee581f000 rw-p 0001e000 fd:01 12959
>  /lib64/ld-2.12.1.so
> 3ee581f000-3ee5820000 rw-p 00000000 00:00 0
> 3ee5a00000-3ee5b75000 r-xp 00000000 fd:01 18799
>  /lib64/libc-2.12.1.so
> 3ee5b75000-3ee5d75000 ---p 00175000 fd:01 18799
>  /lib64/libc-2.12.1.so
> 3ee5d75000-3ee5d79000 r--p 00175000 fd:01 18799
>  /lib64/libc-2.12.1.so
> 3ee5d79000-3ee5d7a000 rw-p 00179000 fd:01 18799
>  /lib64/libc-2.12.1.so
> 3ee5d7a000-3ee5d7f000 rw-p 00000000 00:00 0
> 3ee5e00000-3ee5e83000 r-xp 00000000 fd:01 19168
>  /lib64/libm-2.12.1.so
> 3ee5e83000-3ee6082000 ---p 00083000 fd:01 19168
>  /lib64/libm-2.12.1.so
> 3ee6082000-3ee6083000 r--p 00082000 fd:01 19168
>  /lib64/libm-2.12.1.so
> 3ee6083000-3ee6084000 rw-p 00083000 fd:01 19168
>  /lib64/libm-2.12.1.so
> 3ee6200000-3ee6202000 r-xp 00000000 fd:01 19541
>  /lib64/libdl-2.12.1.so
> 3ee6202000-3ee6402000 ---p 00002000 fd:01 19541
>  /lib64/libdl-2.12.1.so
> 3ee6402000-3ee6403000 r--p 00002000 fd:01 19541
>  /lib64/libdl-2.12.1.so
> 3ee6403000-3ee6404000 rw-p 00003000 fd:01 19541
>  /lib64/libdl-2.12.1.so
> 3ee6600000-3ee6617000 r-xp 00000000 fd:01 18802
>  /lib64/libpthread-2.12.1.so
> 3ee6617000-3ee6816000 ---p 00017000 fd:01 18802
>  /lib64/libpthread-2.12.1.so
> 3ee6816000-3ee6817000 r--p 00016000 fd:01 18802
>  /lib64/libpthread-2.12.1.so
> 3ee6817000-3ee6818000 rw-p 00017000 fd:01 18802
>  /lib64/libpthread-2.12.1.so
> 3ee6818000-3ee681c000 rw-p 00000000 00:00 0
> 3ee9600000-3ee9616000 r-xp 00000000 fd:01 23623
>  /lib64/libgcc_s-4.4.4-20100630.so.1
> 3ee9616000-3ee9815000 ---p 00016000 fd:01 23623
>  /lib64/libgcc_s-4.4.4-20100630.so.1
> 3ee9815000-3ee9816000 rw-p 00015000 fd:01 23623
>  /lib64/libgcc_s-4.4.4-20100630.so.1
> 3eea200000-3eea2e9000 r-xp 00000000 fd:01 23624
>  /usr/lib64/libstdc++.so.6.0.13
> 3eea2e9000-3eea4e9000 ---p 000e9000 fd:01 23624
>  /usr/lib64/libstdc++.so.6.0.13
> 3eea4e9000-3eea4f0000 r--p 000e9000 fd:01 23624
>  /usr/lib64/libstdc++.so.6.0.13
> 3eea4f0000-3eea4f2000 rw-p 000f0000 fd:01 23624
>  /usr/lib64/libstdc++.so.6.0.13
> 3eea4f2000-3eea507000 rw-p 00000000 00:00 0
> 7fc39ad73000-7fc39b751000 rw-p 00000000 00:00 0
> 7fc39b751000-7fc39b765000 r-xp 00000000 fd:00 13766356
>  /home/kevin/kitware/ITK_Build/bin/libitkzlib.so.4.0.0
> 7fc39b765000-7fc39b965000 ---p 00014000 fd:00 13766356
>  /home/kevin/kitware/ITK_Build/bin/libitkzlib.so.4.0.0
> 7fc39b965000-7fc39b966000 rw-p 00014000 fd:00 13766356
>  /home/kevin/kitware/ITK_Build/bin/libitkzlib.so.4.0.0
> 7fc39b966000-7fc39b968000 r-xp 00000000 fd:00 13766680
>  /home/kevin/kitware/ITK_Build/bin/libITKznz.so.4.0.0
> 7fc39b968000-7fc39bb67000 ---p 00002000 fd:00 13766680
>  /home/kevin/kitware/ITK_Build/bin/libITKznz.so.4.0.0
> 7fc39bb67000-7fc39bb68000 rw-p 00001000 fd:00 13766680
>  /home/kevin/kitware/ITK_Build/bin/libITKznz.so.4.0.0
> 7fc39bb68000-7fc39bb69000 rw-p 00000000 00:00 0
> 7fc39bb69000-7fc39bb89000 r-xp 00000000 fd:00 13766805
>  /home/kevin/kitware/ITK_Build/bin/libITKniftiio.so.4.0.0
> 7fc39bb89000-7fc39bd89000 ---p 00020000 fd:00 13766805
>  /home/kevin/kitware/ITK_Build/bin/libITKniftiio.so.4.0.0
> 7fc39bd89000-7fc39bd8a000 rw-p 00020000 fd:00 13766805
>  /home/kevin/kitware/ITK_Build/bin/libITKniftiio.so.4.0.0
> 7fc39bd8a000-7fc39bdb0000 r-xp 00000000 fd:00 13766427
>  /home/kevin/kitware/ITK_Build/bin/libITKEXPAT.so.4.0.0
> 7fc39bdb0000-7fc39bfb0000 ---p 00026000 fd:00 13766427
>  /home/kevin/kitware/ITK_Build/bin/libITKEXPAT.so.4.0.0
> 7fc39bfb0000-7fc39bfb2000 rw-p 00026000 fd:00 13766427
>  /home/kevin/kitware/ITK_Build/bin/libITKEXPAT.so.4.0.0
> 7fc39bfb2000-7fc39bfda000 r-xp 00000000 fd:00 13766792
>  /home/kevin/kitware/ITK_Build/bin/libITKDICOMParser.so.4.0.0Aborted
>
> Without streaming both read/write programs succeed but the scalar
> program prints the
> "N3itk18SpatialOrientation31ValidCoordinateOrientationFlagsEfound"
> warning once.
>
> Code and image headers attached.
>
> _____________________________________
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>
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Luis Ibanez | 1 Dec 2010 04:54
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Re: Questions not in FAQ

Hi TJ,

ITK builds in multiple platforms,

Most flavors of Linux, Mac, and Windows.

     and even in the iPhone / iPad    :-)

See the Nightly builds in our Dashboard:
http://public.kitware.com/dashboard.php?name=itk

ITK is a C++ library for image segmentation and registration.

ITK is independent of MIDAS,
which is a image database system.

Sometimes we store in MIDAS images that are
commonly used by the community of ITK users.

With ITK you can do image processing of N-Dimensional
images, perform image segmentation and image registration,
including deformable, multi-modality and multi-resolution
registration.

Please look at the Getting Starting Tutorial:
http://www.itk.org/CourseWare/Training/GettingStarted-I.pdf

and further tutorials:
http://www.itk.org/ITK/help/tutorials.html

In what file format have you stored those ultrasound images ?

ITK will read well formatted DICOM files...

    Regards,

          Luis

------------------------------------------------------------
On Tue, Nov 16, 2010 at 1:32 PM, TJ <x0142582 <at> ti.com> wrote:
>
>
> Hi,
>
> I am new to this list and had a few questions not covered in the FAQ.
>
> First, there is no mention of a Linux version/branch?  Is there one?  Is
> there a specific reason for Windows only support?  How hard does it appear> to be to port to Linux (Ubuntu)?
>
> Second, I'm trying to figure out where ITK ends and other tools begin. I am
> familiar with TI's MIDAS platform (see link below) but am having trouble
> understanding how far reaching is ITK?  Will it read many ultrasound files,
> etc?
>
> Thanks in advance!!
>
> Tim
>
> https://gforge.ti.com/gf/project/med_ultrasound/
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
_____________________________________
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Luis Ibanez | 1 Dec 2010 04:57
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Gravatar

Re: ITK 3.20 + gdcm 2.0.16 (with VTK support) = cmake config problem

Hi Mario,

This problem was fixed recently in ITKv4

Please see the patch below:

git show 93833edb2294c0190af9e6c0de26e9485399a7d3

~/src/ITK/Utilities/MetaIO
commit 93833edb2294c0190af9e6c0de26e9485399a7d3
Author: ITK Robot <itkrobot <at> kitware.com>
Date:   Thu Jul 22 10:54:04 2010 -0400

    r2796 aylward | 2010-07-22T14:53:45.146190Z
    BUG: Changed from VTK_VERSION to VTK_SOURCE_DIR to determine if
being compiled within VTK or ITK.

diff --git a/Utilities/MetaIO/CMakeLists.txt b/Utilities/MetaIO/CMakeLists.txt
index 1f368f0..757bfc6 100644
--- a/Utilities/MetaIO/CMakeLists.txt
+++ b/Utilities/MetaIO/CMakeLists.txt
 <at>  <at>  -9,11 +9,14  <at>  <at> 
 # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 # See the License for more information.
 #=============================================================================
-IF(VTK_VERSION)
+IF(VTK_SOURCE_DIR)
+
   SET(METAIO_FOR_VTK 1)
   MARK_AS_ADVANCED( METAIO_FOR_VTK )
   SET(METAIO_NAMESPACE "vtkmetaio")
-ELSE(VTK_VERSION)
+
+ELSE(VTK_SOURCE_DIR)
+
   SET(METAIO_FOR_ITK 1)
   MARK_AS_ADVANCED( METAIO_FOR_ITK )
   SET(METAIO_NAMESPACE "ITKMetaIO")
 <at>  <at>  -23,7 +26,7  <at>  <at>  ELSE(VTK_VERSION)
     INCLUDE_DIRECTORIES(${ITK_LIBXML2_INCLUDE_DIR})
   ENDIF(ITK_USE_LIBXML2)

-ENDIF(VTK_VERSION)
+ENDIF(VTK_SOURCE_DIR)

 PROJECT( ${METAIO_NAMESPACE} )

Regards,

      Luis

---------------------------------------------------
On Mon, Nov 22, 2010 at 6:57 AM, Mario Ceresa <mrceresa <at> gmail.com> wrote:
> Hello all!
> I have the following error during ITK 3.20 compilation on Fedora 14 x86_64:
>
> CMake Error at Utilities/MetaIO/CMakeLists.txt:115 (INSTALL):
>  install TARGETS given no LIBRARY DESTINATION for shared library target
>  "vtkmetaio".
>
> These are the cmake parameters used for the build:
>
> cmake -DBUILD_SHARED_LIBS:BOOL=ON \
>       -DBUILD_EXAMPLES:BOOL=ON \
>       -DCMAKE_BUILD_TYPE:STRING="Release"\
>       -DCMAKE_VERBOSE_MAKEFILE=OFF\
>       -DBUILD_TESTING=OFF\
>       -DITK_USE_ORIENTED_IMAGE_DIRECTION:BOOL=ON \
>       -DITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE:BOOL=ON \
>       -DITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY=ON \
>       -DITK_USE_REVIEW:BOOL=ON \
>       -DITK_USE_PATENTED:BOOL=OFF \
>       -DITK_USE_SYSTEM_TIFF=ON \
>       -DITK_USE_SYSTEM_PNG=ON \
>       -DITK_USE_SYSTEM_ZLIB=ON \
>       -DITK_USE_SYSTEM_LIBXML2=ON \
>       -DITK_USE_SYSTEM_GDCM=ON \
>       -DITK_USE_SYSTEM_VXL=OFF \
>       -DITK_USE_SYSTEM_EXPAT=ON .
>
> It seems that the variable VTK_INSTALL_LIB_DIR_CM24 is not defined.
> I use gdcm 2.0 from the Fedora repositories. It has the vtk support enabled.
>
> I would be very grateful if you could help me on the subject :)
>
> With best regards,
>
> Mario
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
_____________________________________
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Luis Ibanez | 1 Dec 2010 05:09
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Gravatar

Re: ITKFlipImageFilter does not reset origin to (0, 0)

Emma,

   "Glimpsing at the Source leaves no doubt..."

ITK/Code/BasicFilters/itkRegionOfInterestImageFilter.txx

lines:121-125

  // Correct origin of the extracted region.
  IndexType roiStart( m_RegionOfInterest.GetIndex() );
  typename Superclass::OutputImageType::PointType outputOrigin;
  inputPtr->TransformIndexToPhysicalPoint(roiStart, outputOrigin);
  outputPtr->SetOrigin(outputOrigin);

and

ITK/Code/BasicFilters/itkFlipImageFilter.txx
lines 118-133

  inputPtr->TransformIndexToPhysicalPoint(newIndex, outputOrigin);

  // Finally, flip about the origin if needed
  if ( m_FlipAboutOrigin )
    {
    for ( j = 0; j < ImageDimension; j++ )
      {
      if ( m_FlipAxes[j] )
        {
        outputOrigin[j] *= -1;
        }
      }
    }

  outputPtr->SetDirection(inputDirection * flipMatrix);
  outputPtr->SetOrigin(outputOrigin);

Most ITK filters produce a new image as output,
but some can reuse the input image in order to
store the output of the filter. These are the filters
deriving from the InPlace filter.

Full list here:
http://www.itk.org/Doxygen/html/classitk_1_1InPlaceImageFilter.html

Note that using InPlace is incompatible with using
the ReleaseDataFlag().

    Regards,

          Luis

--------------
On Wed, Nov 24, 2010 at 8:54 PM, Emma Ryan <eryanvtk <at> yahoo.com> wrote:
> Hello all,
>
>   I'm trying to crop and then flip an image about the Y-axis.  I use the
> RegionOfInterestFilter and the FlipImageFilter.
> I'm having trouble understanding the process.   I have found one previous
> posts but the explanation is not clear.
>
> 1. Do itk filters work with a copy of the image or the image itself ?
>     I thought they worked with a copy of the image, since
> filter->ReleaseDataFlagOn()  would release the original image space.
> Filter->GetOutput() then will return the copy.
>
> 2. for a 500 * 1000 image, after Cropping to 500 * 600 (i.e crop along
> Y-axis from 200 - 800) and Flip, the GetOrigin() returns (0, -800).  Sure I
> can map the indices. But why do I have to ?
> if new_image = filp->GetOutput(), and size of new_image is 500 * 600.  Then
> why is this mapping necessary ?   How can I avoid  it ?
>
> 3. should the flip->ReleaseDataFlagOn(); be used or not ?  What will it do ?
> Irrespective of whether I leave it on of off, I seem to be losing the
> reference to original image.
>
>  Any suggestions are welcome. I have attached the appropriate code segment.
>
>
> Thank you,
> Emma
>
>     ImageType::SizeType roi_size =
> image->GetLargestPossibleRegion().GetSize();
>     itk::Point<float, 2> roi_origin = image->GetOrigin();
>     ImageType::IndexType roi_index;
>     roi_index[0] = roi_origin[0];
>     roi_index[1] = roi_origin[1] + 200;
>     roi_size[1]    = 600;
>     ImageType::RegionType roi_region;
>     roi_region.SetIndex(roi_index);
>     roi_region.SetSize(roi_size);
>
>     typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> ROIType;
>     ROIType::Pointer p_roi_filter = ROIType::New();
>     p_roi_filter->SetRegionOfInterest(roi_region);
>     p_roi_filter->SetInput(image);
>     p_roi_filter->Update();
>
>     flip->SetInput(p_roi_filter->GetOutput());
>     //flip->ReleaseDataFlagOn();
>     flipAxesSet=flip->GetFlipAxes();
>     flipAxesSet[1]=true;
>     flip->SetFlipAxes(flipAxesSet);
>     flip->Update();
>
>     ImageType::Pointer new_image = flip->GetOutput();
>
>
>
> ________________________________
> From: "insight-users-request <at> itk.org" <insight-users-request <at> itk.org>
> To: insight-users <at> itk.org
> Sent: Wed, November 24, 2010 9:00:17 AM
> Subject: Insight-users Digest, Vol 79, Issue 28
>
> Send Insight-users mailing list submissions to
>     insight-users <at> itk.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>     http://www.itk.org/mailman/listinfo/insight-users
> or, via email, send a message with subject or body 'help' to
>     insight-users-request <at> itk.org
>
> You can reach the person managing the list at
>     insight-users-owner <at> itk.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Insight-users digest..."
>
>
> Today's Topics:
>
>   1. Re: [vtkusers] Interactive seed point selection based on QVTK
>       Widget (urgent request for help!) (Prathamesh Kulkarni)
>   2. Re: 2d 3d registration with multiple 2d images (brian avants)
>   3. reset m_CurrentIteration in itkLBFGSBOptimizer (Mengda Wu)
>   4. Re: ManagedITK compilation problem [was MIDAS    Journal
>       Feedback] (Dan Mueller)
>   5. Re: Constructing a 3D volume from 2D cross section (D?enan Zuki?)
>   6. Re: [vtkusers] Interactive seed point selection    based on QVTK
>       Widget (urgent request for help!) (Xiaopeng Yang)
>   7. Re: [vtkusers] Interactive seed point selection based on QVTK
>       Widget (urgent request for help!) (David Doria)
>   8. Re: 2d 3d registration with multiple 2d images (Karthik Krishnan)
>   9. Simplify a set of points in ITK (Marta Peroni)
>   10. Manual de Configuraci?n ITK, VTK & Borland C++ Builder (en
>       espa?ol ) (olguna <at> cimat.mx)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Nov 2010 11:16:31 -0600
> From: Prathamesh Kulkarni <prathameshmkulkarni <at> gmail.com>
> Subject: Re: [Insight-users] [vtkusers] Interactive seed point
>     selection based on QVTK Widget (urgent request for help!)
> To: yxp233 <at> postech.ac.kr
> Cc: insight-users <at> itk.org, VTK Mailing List <vtkusers <at> vtk.org>
> Message-ID:
>     <AANLkTinpCjCxwq7G5Nf3A8t45jYFqJsoXNQstarCxAuw <at> mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I think the vtkSeedWidget fits well for marking seed points. Have a look at
> http://www.vtk.org/Wiki/VTK/Examples/Cxx/Widgets/vtkSeedWidget for example
> usage.
>
> I have used this inside the QVTKWidget as well.
>
> - Prathamesh
>
> Message: 4
> Date: Tue, 23 Nov 2010 06:02:54 -0500
> From: David Doria <daviddoria <at> gmail.com>
> Subject: Re: [Insight-users] [vtkusers] Interactive seed point
>       selection based on QVTK Widget (urgent request for help!)
> To: Xiaopeng Yang <yxp233 <at> postech.ac.kr>
> Cc: itk <Insight-users <at> itk.org>, vtkusers <at> vtk.org
> Message-ID:
>       <AANLkTimuFS5y157YtpzSWfVerZb8zZ9nsQbM4OLa1Jf1 <at> mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Nov 23, 2010 at 1:35 AM, Xiaopeng Yang <yxp233 <at> postech.ac.kr> wrote:
>> Hello everyone,
>>
>>
>>
>> Greetings!
>>
>>
>>
>> In my program for medical image segmentation, QVTK widget ImageViewer2 is
>> used to visualize the images. Do you know what specific functions in VTK
> or
>> ITK I can use to select and load seed point index to my code by simply
>> clicking a point?
>>
>>
>>
>> I know that if imageplane widget is used, then by clicking a point, the
> seed
>> point index and pixel value can be shown in the screen. But I do not know
>> how to save those values to the code automatically at the same time as
>> clicking that point. Meanwhile, I am not sure it is feasible or not to use
>> imageplane widget in QVTK widget.
>>
>>
>>
>> Since the deadline for my program is approaching, any help will be greatly
>> appreciated!
>>
>>
>>
>> Thank you,
>>
>> Xiaopeng
>
> You may want to look at vtkImageTracerWidget:
> http://www.vtk.org/doc/nightly/html/classvtkImageTracerWidget.html
>
> Here is an example example usage:
> http://www.vtk.org/Wiki/VTK/Examples/Cxx/Widgets/ImageTracerWidget
>
> To get the points you handle one of the events (EndInteractionEvent
> probably) and then use the GetPath function.
>
> Also, there should be no problem using VTK widgets in a QVTK widget.
> Here is an example:
> http://www.vtk.org/Wiki/VTK/Examples/Cxx/Qt/BorderWidget
>
> Good luck,
>
> David
>
>
> ------------------------------
> -------------- next part --------------
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> <http://www.itk.org/pipermail/insight-users/attachments/20101123/ab042e86/attachment-0001.htm>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 23 Nov 2010 13:41:04 -0500
> From: brian avants <stnava <at> gmail.com>
> Subject: Re: [Insight-users] 2d 3d registration with multiple 2d
>     images
> To: "Bertelsen, Alvaro" <abertelsen <at> ceit.es>
> Cc: "insight-users <at> itk.org" <insight-users <at> itk.org>
> Message-ID:
>     <AANLkTin7tvWEkoRZf8LQTbaKYOGsFDcF8jLpy-m1=6y8 <at> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> This is an interesting question.  Registration refactoring will
> address this by formulating the problem as a multi-valued
> optimization.  Is it the case that the 2d images are "in the same
> space"  i.e. already in some physical correspondence to each other?
> If so, then the algorithm would be something like:
>
> - Declare "registration machines" for each of the 2D-3D problems.
> - Registration machines contain the image pairs, optimizers, metrics
> for each problem.
> - Pass the machine set to a multi-resolution , multi-valued
> registration coordinator.
> - The coordinator will determine how to combine the output of each machine.
>
> Would this type of approach work for  you?
>
> On Mon, Nov 22, 2010 at 12:05 PM, Bertelsen, Alvaro <abertelsen <at> ceit.es>
> wrote:
>> Dear ITK users,
>>
>>
>>
>> I am working on the development of an image-guided surgery application,
>> for
>> which I need a library for registration of a 3d image to multiple
>> projections. I know about the classes already included in ITK ?such as
>> RayCastInterpolateImageFunction- and the extended library developed by
>> Steininger et al.
>>
>> (http://ibia.umit.at/ResearchGroup/Phil/web/Simple2D3DRegistrationFramework.html).
>> However, these do not fit our needs as they are limited to a single 2d
>> image
>> and we are interested in handling an arbitrary number of them.
>>
>>
>>
>> I have searched in the mailing list and found some other people asking the
>> same question, the last one on April 2006 (unless I have missed a more
>> recent one). So, does anyone know about an ITK extension for what I need?
>> Or, is there a way (which I am not aware of) to make ITK handle multiple
>> fixed (2d) images?
>>
>>
>>
>> Any help you could provide me will be greatly appreciated.
>>
>> Yours sincerely,
>>
>>
>>
>> ?lvaro Bertelsen
>>
>> CEIT, University of Navarra, Spain
>>
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
>>
>>
>
>
>
> --
> ?????
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 23 Nov 2010 17:26:39 -0800
> From: Mengda Wu <wumengda <at> gmail.com>
> Subject: [Insight-users] reset m_CurrentIteration in
>     itkLBFGSBOptimizer
> To: Insight-users <at> itk.org
> Message-ID:
>     <AANLkTinKa2PYR4mbsg66nNXjej1mUX75A49MzRY1ZZ8b <at> mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>
>   I found a small bug which can be annoying in some cases. If the same
> LBFGSBOptimizer is used for BSpline-based deformable registration twice
> (e.g. first in coarser grid and then in finer grid),
> the initial output of the second registration will give the final iteration
> number of the first registration.
>
>   I am wondering if there is a way to reset m_CurrentIteration in
> itkLBFGSBOptimizer. Also, the variable m_InfinityNormOfProjectedGradient has
> the same issue.
>
> Thanks,
> Mengda
> -------------- next part --------------
> An HTML attachment was scrubbed...
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>
> ------------------------------
>
> Message: 4
> Date: Wed, 24 Nov 2010 11:19:35 +0100
> From: Dan Mueller <dan.muel <at> gmail.com>
> Subject: Re: [Insight-users] ManagedITK compilation problem [was MIDAS
>     Journal Feedback]
> To: bergy <at> ukr.net
> Cc: Insight Users <insight-users <at> itk.org>,    Julien Jomier
>     <julien.jomier <at> kitware.com>
> Message-ID:
>     <AANLkTinD8zV-pkJKSRCNQz5tMygch_Neff1cs5epUuFm <at> mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi bergy,
>
> I will try to help with your ManagedITK compilation problem, but you
> will need to provide some more information.
>
> A. What version of ManagedITK are you using?
> You should use this version:
> http://manageditk.googlecode.com/files/ManagedITK-src-3.20.0.0.zip
>
> B. What version of ITK are you using?
> You should use this version:
> http://voxel.dl.sourceforge.net/sourceforge/itk/InsightToolkit-3.20.0.zip
>
> C. What steps did you follow for compilation?
> You should follow the steps list in section 3.2 here:
> http://manageditk.googlecode.com/files/ManagedITK-article.pdf
>
> >From the error messages you reported, it could be that you missed step 6:
> ===================
> 6. Convert to Managed Projects: Before opening the projects, run the
> FinishCMake.bat file located
> in the build folder. Because CMake does not support managed projects,
> this batch file
> is required to convert the generated vcproj files into managed projects.
> ===================
> Did you run FinishCMake.bat?
>
> Aside: In the future, please use the Insight users
> (insight-users <at> itk.org) mailing list for ITK/ManagedITK questions, see
> here: http://www.itk.org/mailman/listinfo/insight-users
> Aside: I have stopped development on ManagedITK. The next version of
> ITK (version 4) will include internal support for C# wrapping. This
> will be ready early- to mid-2011.
>
> Please let me know the answer to these questions.
>
> Regards, Dan
> dan.muel <at> gmail.com
>
> On 23 November 2010 20:41, Julien Jomier <julien.jomier <at> kitware.com> wrote:
>> Dan,
>>
>> Could you answer this question?
>>
>> Thanks,
>> Julien
>>
>> -------- Original Message --------
>> Subject: MIDAS Journal Feedback
>> Date: Tue, 23 Nov 2010 06:35:31 -0500
>> From: webmaster <at> insightsoftwareconsortium.org
>> To: webmaster <at> insightsoftwareconsortium.org
>>
>>
>> MIDAS Journal Feedback from bergy <at> ukr.net
>>
>> Where:
>> What happened: I'm working with Visual Studio 2010 under Windows 7 x64.
>> I'm
>> trying to use ManagedITK in my magister scince work. Because I'm using C#
>> (more faster developing than C++), I chose ManagedITK.
>> I've downloaded, configured and builded ITK. The next step is to build
>> ManagedITK. And I just can not cope with two errors during building
>> ManagedITK:
>> 1. There wasn't /clr command line flag. When I added it another error
>> comming out:
>> ?Command line error D8016: '/clr' and '/EHs' command-line options are
>> incompatible
>>
>> 2. a lot of errors:
>> fatal error C1192: #using failed on
>>
>> 'E:\Work\Magister\ManagedITK\ManagedITKBin-3.6.0.2\bin\Debug\ManagedITK.Common.dll
>>
>> and
>>
>> fatal error C1083: Cannot open source file:
>> 'E:/Work/Magister/ManagedITK/ManagedITKBin-3.6.0.2/bin/Debug': Permission
>> denied
>>
>> I can not understand why there is some "Permission denied" on that folder.
>> I
>> tried to run VS 2010 as an administrator and it didn't help.
>>
>> System: Mozilla/5.0 (Windows; U; Windows NT 6.1; uk; rv:1.9.2.12)
>> Gecko/20101026 Firefox/3.6.12
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 24 Nov 2010 14:01:22 +0100
> From: D?enan Zuki? <dzenanz <at> gmail.com>
> Subject: Re: [Insight-users] Constructing a 3D volume from 2D cross
>     section
> To: Zein Salah <zeinsalah <at> gmail.com>
> Cc: insight-users <at> itk.org
> Message-ID:
>     <AANLkTim7HdNfF-Q6+jmaU=k6azYmEDdMjy6M9jtf_e9G <at> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> perhaps you can convert those slices into DICOM images (if they are in
> that format already just put them all in one series, somehow), and
> then pass them as one series to ITK's DICOM image reader.
>
> HTH,
> D?enan
>
> On Wed, Nov 3, 2010 at 19:56, Zein Salah <zeinsalah <at> gmail.com> wrote:
>> Hello everybody,
>>
>> I have a set of 2D cross sections, originating from an ultrasound
>> scanner, together
>> with their position and rotation data. The sections are non parallel.
>> I am wondering
>> weather there is a mechanism in ITK to reconstrcut a 3D image from these
>> slices.
>>
>> Thanks in advance,
>>
>> Zein
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
>>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 24 Nov 2010 22:49:50 +0900
> From: "Xiaopeng Yang" <yxp233 <at> postech.ac.kr>
> Subject: Re: [Insight-users] [vtkusers] Interactive seed point
>     selection    based on QVTK Widget (urgent request for help!)
> To: "'David Doria'" <daviddoria <at> gmail.com>
> Cc: 'itk' <Insight-users <at> itk.org>, vtkusers <at> vtk.org
> Message-ID: <016101cb8bde$773d0780$65b71680$ <at> ac.kr>
> Content-Type: text/plain;    charset="utf-8"
>
> Thank you for your help. But are you sure the vtkimagetracerwidget is what I
> need for seed point selection?
>
> Xiaopeng
>
> -----????-----
> ???: David Doria [mailto:daviddoria <at> gmail.com]
> ????: 2010? 11? 23? ??? ?? 8:03
> ???: Xiaopeng Yang
> ??: itk; vtkusers <at> vtk.org
> ??: Re: [vtkusers] Interactive seed point selection based on QVTK Widget
> (urgent request for help!)
>
> On Tue, Nov 23, 2010 at 1:35 AM, Xiaopeng Yang <yxp233 <at> postech.ac.kr> wrote:
>> Hello everyone,
>>
>>
>>
>> Greetings!
>>
>>
>>
>> In my program for medical image segmentation, QVTK widget ImageViewer2 is
>> used to visualize the images. Do you know what specific functions in VTK
>> or
>> ITK I can use to select and load seed point index to my code by simply
>> clicking a point?
>>
>>
>>
>> I know that if imageplane widget is used, then by clicking a point, the
>> seed
>> point index and pixel value can be shown in the screen. But I do not know
>> how to save those values to the code automatically at the same time as
>> clicking that point. Meanwhile, I am not sure it is feasible or not to use
>> imageplane widget in QVTK widget.
>>
>>
>>
>> Since the deadline for my program is approaching, any help will be greatly
>> appreciated!
>>
>>
>>
>> Thank you,
>>
>> Xiaopeng
>
> You may want to look at vtkImageTracerWidget:
> http://www.vtk.org/doc/nightly/html/classvtkImageTracerWidget.html
>
> Here is an example example usage:
> http://www.vtk.org/Wiki/VTK/Examples/Cxx/Widgets/ImageTracerWidget
>
> To get the points you handle one of the events (EndInteractionEvent
> probably) and then use the GetPath function.
>
> Also, there should be no problem using VTK widgets in a QVTK widget.
> Here is an example:
> http://www.vtk.org/Wiki/VTK/Examples/Cxx/Qt/BorderWidget
>
> Good luck,
>
> David
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 24 Nov 2010 08:51:18 -0500
> From: David Doria <daviddoria <at> gmail.com>
> Subject: Re: [Insight-users] [vtkusers] Interactive seed point
>     selection based on QVTK Widget (urgent request for help!)
> To: Xiaopeng Yang <yxp233 <at> postech.ac.kr>
> Cc: itk <Insight-users <at> itk.org>, vtkusers <at> vtk.org
> Message-ID:
>     <AANLkTinNjJd2yonodyjhA4FxnPB1saeOwS4W-NqtLUeC <at> mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Wed, Nov 24, 2010 at 8:49 AM, Xiaopeng Yang <yxp233 <at> postech.ac.kr> wrote:
>> Thank you for your help. But are you sure the vtkimagetracerwidget is what
>> I need for seed point selection?
>>
>> Xiaopeng
>
> As Prathamesh mentioned, you might also consider vtkSeedWidget.
>
> David
>
>
> ------------------------------
>
> Message: 8
> Date: Wed, 24 Nov 2010 20:33:23 +0530
> From: Karthik Krishnan <karthik.krishnan <at> kitware.com>
> Subject: Re: [Insight-users] 2d 3d registration with multiple 2d
>     images
> To: brian avants <stnava <at> gmail.com>
> Cc: "insight-users <at> itk.org" <insight-users <at> itk.org>
> Message-ID:
>     <AANLkTinLdaUmR2yBgHFMkc3Pme00m2++nyE62bggHdM0 <at> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Groupwise registration has similar needs. ie. An API in the metric /
> cost function superclass to take in an array of images.
>
> Perhaps it calls for a another hierarchy deriving from
> SingleValuedCostFunction (for groupwise registration) driven by
> variants of the ImageRegistrationMethod
>
> Thanks
> --
> karthik
>
>
> On Wed, Nov 24, 2010 at 12:11 AM, brian avants <stnava <at> gmail.com> wrote:
>> This is an interesting question. ? Registration refactoring will
>> address this by formulating the problem as a multi-valued
>> optimization. ? Is it the case that the 2d images are "in the same
>> space" ?i.e. already in some physical correspondence to each other?
>> If so, then the algorithm would be something like:
>>
>> - Declare "registration machines" for each of the 2D-3D problems.
>> - Registration machines contain the image pairs, optimizers, metrics
>> for each problem.
>> - Pass the machine set to a multi-resolution , multi-valued
>> registration coordinator.
>> - The coordinator will determine how to combine the output of each
>> machine.
>>
>> Would this type of approach work for ?you?
>>
>> On Mon, Nov 22, 2010 at 12:05 PM, Bertelsen, Alvaro <abertelsen <at> ceit.es>
>> wrote:
>>> Dear ITK users,
>>>
>>>
>>>
>>> I am working on the development of an image-guided surgery application,
>>> for
>>> which I need a library for registration of a 3d image to multiple
>>> projections. I know about the classes already included in ITK ?such as
>>> RayCastInterpolateImageFunction- and the extended library developed by
>>> Steininger et al.
>>>
>>> (http://ibia.umit.at/ResearchGroup/Phil/web/Simple2D3DRegistrationFramework.html).
>>> However, these do not fit our needs as they are limited to a single 2d
>>> image
>>> and we are interested in handling an arbitrary number of them.
>>>
>>>
>>>
>>> I have searched in the mailing list and found some other people asking
>>> the
>>> same question, the last one on April 2006 (unless I have missed a more
>>> recent one). So, does anyone know about an ITK extension for what I need?
>>> Or, is there a way (which I am not aware of) to make ITK handle multiple
>>> fixed (2d) images?
>>>
>>>
>>>
>>> Any help you could provide me will be greatly appreciated.
>>>
>>> Yours sincerely,
>>>
>>>
>>>
>>> ?lvaro Bertelsen
>>>
>>> CEIT, University of Navarra, Spain
>>>
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.html
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://www.itk.org/mailman/listinfo/insight-users
>>>
>>>
>>
>>
>>
>> --
>> ?????
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
>>
>
>
> ------------------------------
>
> Message: 9
> Date: Wed, 24 Nov 2010 17:17:48 +0100
> From: Marta Peroni <m.peroni <at> gmail.com>
> Subject: [Insight-users] Simplify a set of points in ITK
> To: ITK Users <insight-users <at> itk.org>
> Cc: Luis Ibanez <luis.ibanez <at> kitware.com>
> Message-ID:
>     <AANLkTimNPYev6x2FCw=NKyZ8AiPZR=0_vqbFOF7r6Q-N <at> mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi!
> I have a kind of "dummy" problem. I do need to select a subset of point
> cloud describing the contour of a structure (the points are previously
> derived with the ITK Review implementation of Marching Squares and therefore
> I do have *lots* of points).
> I found a very nice implementation of this in CGAL Random_Simplify_Points,
> but unfortunately I cannot include the whole library in my project.
> So here it comes the question:
> I did store my points (x,y,z) in a PointsContainer (as in PointSet2.cxx).
> Now in order for the algorithm to work, I need to randomly shuffle /
> randomly extract from the container (shuffle would be the best option).
> Is there something similar to itk::ImageRandomNonRepeatingIteratorWithIndex
> but for points containers?and/or a shuffle method?
> thanks a lot
> Marta
> --
> *******************************************************************
> Marta Peroni
> PhD Student - Bioengineering department - Politecnico di Milano (IT)
>
> contacts:
> mail: marta.peroni <at> mail.polimi.it , m.peroni <at> gmail.com
> mobile: +393488202136 (IT) +16178186365 (US)
> office: +39 02 2399 9022
>
> ********************************************************************
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 10
> Date: Wed, 24 Nov 2010 10:25:45 -0600
> From: olguna <at> cimat.mx
> Subject: [Insight-users] Manual de Configuraci?n ITK, VTK & Borland
>     C++ Builder (en espa?ol )
> To: insight-users <at> itk.org, vtkusers <at> vtk.org
> Message-ID:
>     <5d7e2c715bad80e8ac4852a0e710bcea.squirrel <at> correo.cimat.mx>
> Content-Type: text/plain;charset=iso-8859-1
>
> Message written in Spanish with the intention to communicate with Spanish
> speakers, without attempting to exclude anyone.
>
> Saludos Usuarios de ITK & VTK y quienes aun trabajen en Borland C++
> Builder 5.3 (desde 2008 C++ Builder pertenece a Embarcadero), hago de su
> conocimiento y pongo a su disposici?n un manual de instalaci?n/compilaci?n
> de BCB, ITK & VTK, en espa?ol, lo pueden encontrar en
> http://effort-2-improve.wikispaces.com/BCBITKVTK, a manera de
> agradecimiento por la disponibilidad de estas librer?as y de la buena
> asesor?a recibida cuando realizaba mis primeros pasos en dicha plataforma.
>
> Espero les sea de utilidad, ATTE:
> L. en M. Oscar Guti?rrez Luna
>
> Greetings Members of ITK & VTK and who are still working in Borland C + +
> Builder 5.3 (since 2008 C + + Builder belongs to Embarcadero), I put at
> its disposal a manual installation / compilation of BCB, ITK & VTK (only
> in Spanish), can be found on
> http://effort-2-improve.wikispaces.com/BCBITKVTK, as an appreciation for
> the availability of these libraries and good advice received while
> conducting my first steps on that platform.
>
> I hope this will be useful
> L. in M. Oscar Guti?rrez Luna
>
> "One can't learn anything so well as by experiencing it oneself"
>
> Albert Einstein
>
>
> "...la sabiduria no se transmite. La ciencia que el sabio intenta
> comunicar suena siempre a locura." Hermann Hesse. SIDDHARTHA
>
>
>
> ------------------------------
>
> _______________________________________________
> Insight-users mailing list
> Insight-users <at> itk.org
> http://www.itk.org/mailman/listinfo/insight-users
>
>
> End of Insight-users Digest, Vol 79, Issue 28
> *********************************************
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
>
_____________________________________
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Please keep messages on-topic and check the ITK FAQ at:
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Follow this link to subscribe/unsubscribe:
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Gmane