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<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial>Hi Pierre,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial>elastix does not offer functionality for point or surface
registration, it's currently all about intensity-based
registration.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial>Since the ITK offers functionality to register point sets,
however, it may be relatively straightforward to incorporate this in elastix. If
you are interested, I'll be happy to guide you through the process of adding
components to elastix.</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial>Regards,</FONT></SPAN></DIV>
<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial></FONT></SPAN> </DIV>
<DIV dir=ltr align=left><SPAN class=796531607-19082009><FONT color=#0000ff
size=2 face=Arial>Marius</FONT></SPAN></DIV><BR>
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<FONT size=2 face=Tahoma><B>From:</B> Pierre JUILLARD
[mailto:pierre.juillard@gmail.com] <BR><B>Sent:</B> Tuesday, August 18, 2009
7:24 PM<BR><B>To:</B> Staring, M. (LKEB)<BR><B>Cc:</B>
insight-users@itk.org<BR><B>Subject:</B> Re: [Insight-users] New elastix
release 4.2<BR></FONT><BR></DIV>
<DIV></DIV>Hi Marius,<BR><BR>Thanks to share on the ITK mailing this news and
this huge work.<BR>I had an overview of the manual and it doesn't seem so,
also I prefer to ask: does elastix offer some functionalities to handle
registration of 3D point cloud or 3D surfaces?<BR>Or is it foreseen in a near
future?<BR><BR>Thank you in advance for the hints.<BR>Best
regards,<BR><BR>Pierre<BR><BR><BR><BR>
<DIV class=gmail_quote>2009/8/18 <SPAN dir=ltr><<A
href="mailto:M.Staring@lumc.nl">M.Staring@lumc.nl</A>></SPAN><BR>
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<DIV>
<DIV dir=ltr align=left>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>Dear
list-subscribers,</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT face=Arial><FONT color=#0000ff><FONT size=2>We are proud to
announce a new release of elastix: elastix 4.2
!</FONT></FONT></FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><SPAN><FONT face=Arial><FONT color=#0000ff size=2>Elastix is a
software package for image registration, based on the ITK. The software
consists of a collection of algorithms that are commonly used to solve
medical image registration problems. The modular design of elastix allows
the user to quickly configure, test, and compare different registration
methods for a specific application. In addition to the existing ITK image
registration classes, elastix implements new functionality. The most
important enhancements are</FONT></FONT></SPAN></SPAN></DIV>
<DIV><SPAN><SPAN></SPAN></SPAN> </DIV>
<DIV><SPAN><SPAN></SPAN></SPAN><SPAN><SPAN><FONT face=Arial><FONT
color=#0000ff><FONT size=2>- A modular framework for sampling
strategies.</FONT></FONT></FONT></SPAN></SPAN></DIV>
<DIV><SPAN><SPAN><FONT color=#0000ff size=2 face=Arial>- More
optimisers: Kiefer-Wolfowitz, Robbins-Monro, adaptive
</FONT></SPAN></SPAN><SPAN><SPAN><FONT color=#0000ff size=2
face=Arial>stochastic gradient descent, evolutionary
strategy.</FONT></SPAN></SPAN></DIV>
<DIV><SPAN><SPAN><FONT color=#0000ff size=2 face=Arial>- Complete rework of
existing ITK optimisers, adding more user control
</FONT></SPAN></SPAN><SPAN><SPAN><FONT color=#0000ff size=2 face=Arial>and
better error handling: quasi-Newton, nonlinear conjugate
gradient.</FONT></SPAN></SPAN></DIV>
<DIV><SPAN><SPAN><FONT color=#0000ff size=2
face=Arial>- </FONT></SPAN></SPAN><SPAN><SPAN><FONT color=#0000ff
size=2 face=Arial>Several new or more flexible cost functions: (normalised)
mutual </FONT><FONT color=#0000ff size=2 face=Arial>information, implemented
with Parzen windowing similar to [45], multifeature </FONT><FONT
color=#0000ff size=2 face=Arial>$B&A(B-mutual information, bending energy penalty
term, rigidity </FONT><FONT color=#0000ff size=2 face=Arial>penalty
term.</FONT></SPAN></SPAN></DIV>
<DIV><SPAN><SPAN><FONT face=Arial><FONT color=#0000ff size=2>- The ability
to concatenate any number of geometric
transformations.</FONT></FONT></SPAN></SPAN></DIV>
<DIV><SPAN><SPAN><FONT face=Arial><FONT color=#0000ff size=2>- The
transformations support computation of not only $B"_(BT/$B"_&L(B, but also
</FONT></FONT><FONT color=#0000ff size=2 face=Arial>of spatial derivatives
$B"_(BT/$B"_(Bx and $B"_(B2T/$B"_(Bx2, and their derivatives to </FONT><FONT color=#0000ff
size=2 face=Arial>$B&L(B, frequently required for the computation of
regularisation terms. Additionally, </FONT><FONT color=#0000ff size=2
face=Arial>the compact support of certain transformations is integrated
</FONT><FONT color=#0000ff size=2 face=Arial>more
generally.</FONT></SPAN></SPAN></DIV>
<DIV><SPAN><SPAN><FONT face=Arial><FONT color=#0000ff size=2>- Linear
combinations of cost functions, instead of just a single cost
</FONT></FONT><FONT color=#0000ff size=2
face=Arial>function.</FONT></SPAN></SPAN></DIV>
<DIV><SPAN><SPAN><FONT color=#0000ff size=2
face=Arial></FONT></SPAN></SPAN> </DIV>
<DIV><FONT face=Arial><FONT color=#0000ff><FONT
size=2><SPAN><SPAN> </SPAN></SPAN><SPAN>Elastix can be
downloaded<SPAN> </SPAN>from the website<SPAN>, under the very open BSD
license, see</SPAN>:</SPAN></FONT></FONT></FONT></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>
</FONT><A href="http://elastix.isi.uu.nl/" target=_blank><FONT size=2
face=Arial>http://elastix.isi.uu.nl/</FONT></A></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>We have updated quite some
components in this new release<SPAN> compared to elastix 4.1</SPAN>, and
also added a few. The most important changes are:</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>- The implementation of
spatial derivatives in all transform classes. This enables the computation
of many regularisation (penalty) terms in a general way.</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>- A general way
of dealing with sparse Jacobians, so that for example much
less B-spline specific code is needed anymore.</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>- The adaptive stochastic
gradient descent (ASGD) optimization routine is now usable for much larger
registration problems. (It used to crash when the number of parameters was
larger than 10 000.)</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>- We added the following
components: WeightedCombinationTransform, SplineKernelTransform (which
implements a ThinPlateSpline, ElasticBodySpline, VolumeSpline, and an
ElasticBodyReciprocalSpline), TransformRigidityPenalty,
TransformBendingEnergyPenalty,
DisplacementMagnitudePenalty.</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>A more complete list of
changes can be found at the website:</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT face=Arial><FONT color=#0000ff><FONT
size=2> </FONT><A
href="http://elastix.isi.uu.nl/whatsnew_04_2.php" target=_blank><FONT
size=2>http://elastix.isi.uu.nl/whatsnew_04_2.php</FONT></A></FONT></FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>If you find any bugs or
have comments on this new release, please contact us through the
mailinglist:</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT face=Arial><FONT color=#0000ff><FONT
size=2> </FONT><A href="mailto:elastix@bigr.nl"
target=_blank><FONT
size=2>elastix@bigr.nl</FONT></A></FONT></FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>We are also looking for a
volunteer to build MacOSX binaries for us, so we can place them on the
website.</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial>Enjoy
elastix!</FONT></SPAN></DIV>
<DIV><SPAN><FONT color=#0000ff size=2 face=Arial></FONT></SPAN> </DIV>
<DIV><FONT face=Arial><SPAN><FONT color=#0000ff><FONT size=2>Stefan Klein
and Marius Staring<SPAN> </SPAN></FONT></FONT></SPAN></FONT></DIV>
<DIV><FONT face=Arial><SPAN><FONT color=#0000ff><FONT
size=2><SPAN></SPAN></FONT></FONT></SPAN></FONT> </DIV></DIV></DIV><BR>_____________________________________<BR>Powered
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