[Insight-developers] RE: Demons voodoo
Miller, James V (Research)
millerjv at crd.ge.com
Fri, 9 Apr 2004 11:14:48 -0400
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Lydia,
I checked in my changes to the DemonsRegistrationFunction on the branch
PDE-Registration. The files affected are
Code/Algorithms/itkDemonsRegistrationFunction.h
Code/Algorithms/itkDemonsRegistrationFunction.txx
Code/Algorithms/itkPDEDeformableRegistrationFilter.txx
Examples/Registration/DeformableRegistration2.cxx
You can test this version on your data and see what impact it has on your
results.
Jim
-----Original Message-----
From: Miller, James V (Research) [mailto:millerjv at crd.ge.com]
Sent: Friday, April 09, 2004 9:58 AM
To: 'Insight-developers (E-mail)'
Subject: [Insight-developers] RE: Demons voodoo
Lydia,
I can use the WarpImageFilter as is. Though I am thinking of writing a
filter that will approximate the inverse of a deformation. There are some
one-to-many/many-to-one issues but we could handle them via an
approximation.
I am going to "try" to create a branch where I can checkin my changes. This
way you can try them on your data and see if you like the results at all.
I'll put my test images in Testing/Data/Input.
In thinking about this more, how about this plan of attack. Why don't you
come up with the definition of "forward mapping" and "reverse mapping" given
a fixed and moving image. You have been thinking about this longer than I
have, so we'll start with whatever definition you come up with.
We'll then document in each of these filters whether they calculate a
forward or reverse mapping. I think we can put a protected flag in the
PDEDeformableRegistrationFilter such that subclasses can indicate to the
PDEDeformableRegistrationFilter whether they calculate a forward or reverse
mapping. The PDEDeformableRegistrationFilter can then implement the pipeline
calls using meta-information from the moving or fixed image, whichever is
appropriate. If we can write routines that can produce either a forward or
reverse mapping, then we'll expose the flag to the user.
There are some other things I'd like to change with the Demons algorithms.
For instance, I would like to add a mode to precompute gradients and
gradient magnitudes of the fixed image so that I can trade off memory for
speed. But I am going to hold off on this until we decide how to handle the
forward/reverse mapping.
I have some other tests I want to run ferret out the differences in the
forward/reverse approaches. I think there may a difference in how the low
end of the intensity range is manipulated.
Jim
-----Original Message-----
From: Lydia Ng [mailto:lng at insightful.com]
Sent: Thursday, April 08, 2004 8:09 PM
To: Miller, James V (Research); Insight-developers (E-mail)
Subject: RE: Demons voodoo
Jim,
Are you able to use the WarpImageFilter as it? Or do you have to modify it
to?
Also, have you seen http://www.inria.fr/rrrt/rr-3706.html
<http://www.inria.fr/rrrt/rr-3706.html> ?
BTW: Could you send me your test code and the toy images? I am wondering if
the current implementation uses moving image derivative instead of the fixed
image that the behavior may be to same as to your suggested changes.
-Lydia
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<BODY lang=3DEN-US style=3D"tab-interval: .5in" vLink=3Dblue =
link=3Dblue>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff =
size=3D2>Lydia,=20
</FONT></SPAN></DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff size=3D2>I =
checked in my=20
changes to the DemonsRegistrationFunction on the branch =
PDE-Registration. =20
The files affected are</FONT></SPAN></DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2>Code/Algorithms/itkDemonsRegistrationFunction.h</FONT></SPAN></=
DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2>Code/Algorithms/itkDemonsRegistrationFunction.txx</FONT></SPAN>=
</DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2>Code/Algorithms/itkPDEDeformableRegistrationFilter.txx</FONT></=
SPAN></DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2>Examples/Registration/DeformableRegistration2.cxx</FONT></SPAN>=
</DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff =
size=3D2>You can test this=20
version on your data and see what impact it has on your=20
results.</FONT></SPAN></DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D464091215-09042004><FONT color=3D#0000ff=20
size=3D2>Jim</FONT></SPAN></DIV>
<BLOCKQUOTE dir=3Dltr style=3D"MARGIN-RIGHT: 0px">
<DIV class=3DOutlookMessageHeader dir=3Dltr align=3Dleft><FONT =
face=3DTahoma=20
size=3D2>-----Original Message-----<BR><B>From:</B> Miller, James V =
(Research)=20
[mailto:millerjv at crd.ge.com]<BR><B>Sent:</B> Friday, April 09, 2004 =
9:58=20
AM<BR><B>To:</B> 'Insight-developers (E-mail)'<BR><B>Subject:</B>=20
[Insight-developers] RE: Demons voodoo<BR><BR></FONT></DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff =
size=3D2>Lydia,=20
</FONT></SPAN></DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff =
size=3D2>I can use the=20
WarpImageFilter as is. Though I am thinking of writing a filter that =
will=20
approximate the inverse of a deformation. There are some=20
one-to-many/many-to-one issues but we could handle them via an=20
approximation.</FONT></SPAN></DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff =
size=3D2>I am going to=20
"try" to create a branch where I can checkin my changes. This =
way you can=20
try them on your data and see if you like the results at=20
all. I'll put my test images in =
Testing/Data/Input.</FONT></SPAN></DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff =
size=3D2>In thinking=20
about this more, how about this plan of attack. Why don't you =
come up=20
with the definition of "forward mapping" and "reverse mapping" given =
a fixed=20
and moving image. You have been thinking about this longer than I =
have, so=20
we'll start with whatever definition you come up with. =20
</FONT></SPAN></DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff =
size=3D2>We'll then=20
document in each of these filters whether they calculate a forward or =
reverse=20
mapping. I think we can put a protected flag in the=20
PDEDeformableRegistrationFilter such that subclasses can indicate to =
the=20
PDEDeformableRegistrationFilter whether they calculate a forward or =
reverse=20
mapping. The PDEDeformableRegistrationFilter can then implement the =
pipeline=20
calls using meta-information from the moving or fixed image, =
whichever is=20
appropriate. If we can write routines that can produce either a =
forward or
reverse mapping, then we'll expose the flag to the user. =20
</FONT></SPAN></DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff =
size=3D2>There are some=20
other things I'd like to change with the Demons algorithms. For =
instance, I would like to add a mode to precompute gradients and =
gradient=20
magnitudes of the fixed image so that I can trade off memory for =
speed. But I=20
am going to hold off on this until we decide how to handle the =
forward/reverse=20
mapping.</FONT></SPAN></DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff =
size=3D2>I have some=20
other tests I want to run ferret out the differences in the =
forward/reverse=20
approaches. I think there may a difference in how the low end =
of the=20
intensity range is manipulated.</FONT></SPAN></DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff=20
size=3D2></FONT></SPAN> </DIV>
<DIV><SPAN class=3D884011113-09042004><FONT color=3D#0000ff=20
size=3D2>Jim</FONT></SPAN></DIV>
<BLOCKQUOTE dir=3Dltr style=3D"MARGIN-RIGHT: 0px">
<DIV class=3DOutlookMessageHeader dir=3Dltr align=3Dleft><FONT =
face=3DTahoma=20
size=3D2>-----Original Message-----<BR><B>From:</B> Lydia Ng=20
[mailto:lng at insightful.com]<BR><B>Sent:</B> Thursday, April 08, =
2004 8:09=20
PM<BR><B>To:</B> Miller, James V (Research); Insight-developers=20
(E-mail)<BR><B>Subject:</B> RE: Demons voodoo<BR><BR></FONT></DIV>
<DIV class=3DSection1>
<P class=3DMsoNormal><FONT face=3DArial color=3Dnavy size=3D2><SPAN =
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial">Jim,<o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal><FONT face=3DArial color=3Dnavy size=3D2><SPAN =
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=3DMsoNormal><FONT face=3DArial color=3Dnavy size=3D2><SPAN =
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">Are you =
able to use=20
the WarpImageFilter as it? Or do you have to modify it=20
to?<o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal><FONT face=3DArial color=3Dnavy size=3D2><SPAN =
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=3DMsoNormal><FONT face=3DArial color=3Dnavy size=3D2><SPAN =
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: Arial">Also, =
have you seen=20
<A=20
=
href=3D"http://www.inria.fr/rrrt/rr-3706.html">http://www.inria.fr/rrrt/=
rr-3706.html</A>?=20
<o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal><FONT face=3DArial color=3Dnavy size=3D2><SPAN =
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=3DMsoNormal style=3D"tab-stops: 328.5pt"><FONT =
face=3DArial color=3Dnavy=20
size=3D2><SPAN style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial">BTW:=20
Could you send me your test code and the toy images? I am wondering =
if the=20
current implementation uses moving image derivative instead of the =
fixed=20
image that the behavior may be to same as to your suggested =
changes.<SPAN=20
style=3D"mso-tab-count: =
1"> =20
</SPAN><o:p></o:p></SPAN></FONT></P>
<P class=3DMsoNormal><FONT face=3DArial color=3Dnavy size=3D2><SPAN =
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial"><o:p> </o:p></SPAN></FONT></P>
<P class=3DMsoNormal><FONT face=3DArial color=3Dnavy size=3D2><SPAN =
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial">-</SPAN></FONT><st1:country-region><st1:place><FONT=20
face=3DArial color=3Dnavy size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial">Lydia</SPAN></FONT></st1:place></st1:country-region><FONT=20
face=3DArial color=3Dnavy size=3D2><SPAN=20
style=3D"FONT-SIZE: 10pt; COLOR: navy; FONT-FAMILY: =
Arial"><o:p></o:p></SPAN></FONT></P></DIV></BLOCKQUOTE></BLOCKQUOTE></BO=
DY></HTML>
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