[ITK] FEM registration
Judisch, Alexandra Lynae
alexandra-judisch at pitt.edu
Tue Oct 6 16:16:24 EDT 2015
I am using the FEM registration filter to register 2 highly deformed images together, but I think it could do better with the inclusion of landmarks. Going though the code, I see that there is a method included to do so, but when I write it up I keep getting segmentation fault 11. Any ideas on what I'm doing wrong?
Thanks!
Alex
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Subject: Community Digest, Vol 25, Issue 7
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Today's Topics:
1. [ITK-users] Demons Registration (stefano serviddio)
2. Re: [ITK-dev] itkStaticConstMacro definition (Matt McCormick)
3. [ITK-users] New Submission: Transitively Consistent and
Unbiased Multi-Image Registration using Numerically Stable
Transformation Synchronisation (MIDAS Journal)
4. Re: [ITK-users] How to Calculate Hessian Matrix from Gradient
Image? (Jakob Weiss)
5. Call a class inside a template class (Constantinus Spanakis)
6. [ITK-users] Problem with configure with 4.8.1 and gcc 5
(Alfonso Castro)
7. Re: [ITK-users] How to Calculate Hessian Matrix from Gradient
Image? (Siddharth Vikal)
----------------------------------------------------------------------
Message: 1
Date: Mon, 05 Oct 2015 16:05:36 +0000
From: stefano serviddio <s.serviddio at gmail.com>
To: "insight-users at itk.org" <insight-users at itk.org>
Subject: [ITK] [ITK-users] Demons Registration
Message-ID:
<CADnakivvri+xDBqmCNa9KSzZ+rcJaT+9XeCK0YZH0MN0L50GYA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
I have a big doubt, Can you say me if there is a case or when demons
registration could fall into a local minimum???
Have you any papers that address this topic???
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Message: 2
Date: Mon, 5 Oct 2015 12:18:50 -0400
From: Matt McCormick <matt.mccormick at kitware.com>
To: Luc Hermitte <luc.hermitte at c-s.fr>
Cc: Insight Developers <insight-developers at itk.org>
Subject: Re: [ITK] [ITK-dev] itkStaticConstMacro definition
Message-ID:
<CALzTN-QKaSsWG-qAaj-zgWxyQ_VGqLquKPsa_CrFxEuzWR3KPw at mail.gmail.com>
Content-Type: text/plain; charset="us-ascii"
Hi Luc,
> I'm currently trying to push code that exploits SFINAE and itk::EnableIf.
Cool :-)
> I have a problem with clang, in C++98 mode, as it barks when we are
> using an unnamed type as a template parameter
> -> "note: unnamed type used in template argument was declared here"
>
> There is an easy fix for it: drop the compatibility to old compilers
> like VC++6 when writing metaprograms. In this case, itkStaticConstMAcro
> shall not generate an enum,
> enum { variable = value }; // (1)
> but
> const static type variable = value; // (2)
>
> I've searched google and gerrit to see why definition (2) has been
> commented out, but I've found nothing. If I understand correctly, in the
> past, a CMake test was used to choose how the macro shall be written.
> This is not the case any more.
Yes, that is also my recollection. But, nobody has just bothered to
update the definition.
> So my questions:
> Does anybody remember/know why definition (2) has been dropped? Can't we
> revert to it (or at least to a conditional definition of
> itkStaticConstMacro) for compilers clang that are pedantically compliant
> to C++98 standard?
> (constexpr will of course be required with C++11 compliant compilers
> used in C++11 (or more) mode)
Yes :-)
> BTW, which is the oldest VC++ compiler officially supported by ITK? Must
> I understand from this that VC++7.1 support has already been dropped
> since 2012?
> (http://www.itk.org/Wiki/ITK_Release_4/Modern_C%2B%2B#Fully_Committed_to_Support)
Correct. The current oldest version of VC++ is 9.
Thanks,
Matt
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Message: 3
Date: Mon, 5 Oct 2015 17:39:03 -0400 (EDT)
From: MIDAS Journal <noreply at insightsoftwareconsortium.org>
To: insight-users at itk.org
Subject: [ITK] [ITK-users] New Submission: Transitively Consistent and
Unbiased Multi-Image Registration using Numerically Stable
Transformation Synchronisation
Message-ID: <20151005213903.162A33D6213B at insight-journal.org>
Content-Type: text/plain; charset="us-ascii"
Hello,
A new submission has been added to the MIDAS Journal.
Title: Transitively Consistent and Unbiased Multi-Image Registration using Numerically Stable Transformation Synchronisation
Authors: Bernard F., Thunberg J., Husch A., Salamanca L., Gemmar P., Hertel F., Goncalves J.
Abstract: Transitive consistency of pairwise transformations is a desirable property of groupwise image registration procedures. The transformation synchronisation method (Bernard et al., 2015) is able to retrieve transitively consistent pairwise transformations from pairwise transformations that are initially not transitively consistent. In the present paper, we present a numerically stable implementation of the transformation synchronisation method for affine transformations, which can deal with very large translations, such as those occurring in medical images where the coordinate origins may be far away from each other. By using this method in conjunction with any pairwise (affine) image registration algorithm, a transitively consistent and unbiased groupwise image registration can be achieved.
Experiments involving the average template generation from 3D brain images demonstrate that the method is more robust with respect to outliers and achieves higher registration accuracy compared to reference-based registration.
Download and review this publication at: http://hdl.handle.net/10380/3526
Generated by the MIDAS Journal
You are receiving this email because you asked to be informed by the MIDAS Journal for new submissions. To change your email preference visit http://www.midasjournal.org/ .
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Message: 4
Date: Mon, 5 Oct 2015 23:09:17 -0700 (MST)
From: Jakob Weiss <weissj at in.tum.de>
To: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] How to Calculate Hessian Matrix from
Gradient Image?
Message-ID: <1444111757164-36288.post at n7.nabble.com>
Content-Type: text/plain; charset="utf-8"
Thank you a lot Matheus, this has been very helpful!
As to the question of using the Jacobian: Since the Hessian s the same as
the Jacobian of the Gradient, this just another equal formulation of the
same problem. I could not find any filter for computing the Jacobian on a
vector volume either, so not really a solution. For example [1] applies a
scheme to make these matrices symmetric.
Cheers,
J
[1] Goch, Caspar J., et al. "Liver vessel segmentation using gradient vector
flow." Bildverarbeitung f?r die Medizin 2011. Springer Berlin Heidelberg,
2011. 104-108.
--
View this message in context: http://itk-users.7.n7.nabble.com/ITK-users-How-to-Calculate-Hessian-Matrix-from-Gradient-Image-tp35400p36288.html
Sent from the ITK - Users mailing list archive at Nabble.com.
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Message: 5
Date: Tue, 6 Oct 2015 12:57:36 +0300
From: Constantinus Spanakis <c.spanakis83 at gmail.com>
To: community at itk.org
Subject: [ITK] Call a class inside a template class
Message-ID:
<CAOZihbchba8PvNT3FJB3nKVTgYdyZgfdCJ=DMHEKibyObBRqaA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hello. I want to call a GaussianImageFilter inside the template class
NormalizedMutualInformation in order to study the spatial information
of the image during the image registration process. However, in order
to study the spatial information the object constructed upon the
GaussianImageFilter must have access in the image data. How can i set
the input of the filter?
PS: I know that the GaussianImageFilter has the SetInput( ) method,
but i don't know what argument I should insert.
------------------------------
Message: 6
Date: Tue, 06 Oct 2015 16:20:24 +0200
From: Alfonso Castro <alfonso.castro at udc.es>
To: insight-users at itk.org
Subject: [ITK] [ITK-users] Problem with configure with 4.8.1 and gcc 5
Message-ID: <1792052.Ej4RIIi5E6 at hinata>
Content-Type: text/plain; charset="us-ascii"
Hi.
I tried to compiled in OpenSuSE Tumbleweed ITK 4.8.1 but I obtained an error
in configure:
CMake Error at /usr/share/cmake/Modules/TestBigEndian.cmake:51 (message):
no suitable type found
Call Stack (most recent call first):
Modules/ThirdParty/VNL/src/vxl/config/cmake/config/CMakeLists.txt:285
(TEST_BIG_ENDIAN)
However, the configuration and compile are without a problem using clang.
The info of gcc version is:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/5/lto-wrapper
Target: x86_64-suse-linux
Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --
mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-
languages=c,c++,objc,fortran,obj-c++,java,ada,go --enable-checking=release --
with-gxx-include-dir=/usr/include/c++/5 --enable-ssp --disable-libssp --
disable-libvtv --enable-libmpx --disable-plugin --with-bugurl=http://
bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --disable-libgcj --with-
slibdir=/lib64 --with-system-zlib --enable-__cxa_atexit --enable-libstdcxx-
allocator=new --disable-libstdcxx-pch --enable-version-specific-runtime-libs
--enable-linker-build-id --enable-linux-futex --program-suffix=-5 --without-
system-libunwind --enable-multilib --with-arch-32=i586 --with-tune=generic --
build=x86_64-suse-linux --host=x86_64-suse-linux
Thread model: posix
gcc version 5.1.1 20150713 [gcc-5-branch revision 225736] (SUSE Linux)
VTK 6.3 compile without a problem using gcc 5.
The info of clang version is:
clang version 3.7.0 (tags/RELEASE_370/final 246586)
Target: x86_64-suse-linux
Thread model: posix
Found candidate GCC installation: /usr/bin/../lib64/gcc/x86_64-suse-linux/4.8
Found candidate GCC installation: /usr/bin/../lib64/gcc/x86_64-suse-linux/5
Found candidate GCC installation: /usr/lib64/gcc/x86_64-suse-linux/4.8
Found candidate GCC installation: /usr/lib64/gcc/x86_64-suse-linux/5
Selected GCC installation: /usr/bin/../lib64/gcc/x86_64-suse-linux/5
Candidate multilib: .;@m64
Selected multilib: .;@m64
Thanks in advance.
Alfonso Castro
Faculty of Computer Science
University of A Coruna
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------------------------------
Message: 7
Date: Tue, 6 Oct 2015 16:59:44 +0100
From: Siddharth Vikal <siddharthvikal at gmail.com>
To: Jakob Weiss <weissj at in.tum.de>
Cc: insight-users at itk.org
Subject: Re: [ITK] [ITK-users] How to Calculate Hessian Matrix from
Gradient Image?
Message-ID:
<CADM22yxMLXb19VJkDcLJ9T4DPNeNiewAGe1vY3t-Cct6CnCHNg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Well, there is a jacobian filter available in ITK that calculates the
jacobian of displacement field (vector) image volume:
http://www.itk.org/Doxygen/html/classitk_1_1DisplacementFieldJacobianDeterminantFilter.html
It returns the jacobin determinant, but one can easily modify it to return
the Jacobian matrix, and then do the eigen value analysis on top of that.
Cheers
On Tue, Oct 6, 2015 at 7:09 AM, Jakob Weiss <weissj at in.tum.de> wrote:
> Thank you a lot Matheus, this has been very helpful!
>
> As to the question of using the Jacobian: Since the Hessian s the same as
> the Jacobian of the Gradient, this just another equal formulation of the
> same problem. I could not find any filter for computing the Jacobian on a
> vector volume either, so not really a solution. For example [1] applies a
> scheme to make these matrices symmetric.
>
> Cheers,
> J
>
> [1] Goch, Caspar J., et al. "Liver vessel segmentation using gradient
> vector
> flow." Bildverarbeitung f?r die Medizin 2011. Springer Berlin Heidelberg,
> 2011. 104-108.
>
>
>
> --
> View this message in context:
> http://itk-users.7.n7.nabble.com/ITK-users-How-to-Calculate-Hessian-Matrix-from-Gradient-Image-tp35400p36288.html
> Sent from the ITK - Users mailing list archive at Nabble.com.
> _____________________________________
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>
> Visit other Kitware open-source projects at
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>
> Kitware offers ITK Training Courses, for more information visit:
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>
> Please keep messages on-topic and check the ITK FAQ at:
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>
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