[Insight-users] Image registration - 2 different initializati
ons
Radhika Sivaramakrishna
radhika.sivaramakrishna at synarc.com
Thu, 15 Jan 2004 11:16:48 -0800
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Hi Luis,
I am really sorry about this. I think I pasted the wrong thing from my
output.
Here it is with the DicomSeries -> Raw -> Analyze run:
Transform center before Initializer 0 0 0
Transform center after Initializer 123.619 150.723 97.2895
Intial Parameters =
[0, 0, 0, 0.661387, 1.31363, -0.631911]
Translationscale = 1000
Here it is with the Dicom series run:
Transform center before Initializer 0 0 0
Transform center after Initializer -2.34973 225.964 219.384
Intial Parameters =
[0, 0, 0, -0.0650073, 1.4008, -2.19123]
Translationscale = 1000
Thanks
Radhika
-----Original Message-----
From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
Sent: Thursday, January 15, 2004 11:12 AM
To: Radhika Sivaramakrishna
Cc: 'insight-users at itk.org'
Subject: Re: [Insight-users] Image registration - 2 different initializati
ons
Hi Radhika,
Sorry... still unclear.
The two initialization values that you
posted in your email look the same to me.
http://www.itk.org/pipermail/insight-users/2004-January/006280.html
Transform center after Initializer -2.34973 225.964 219.384
versus
Transform center after Initializer -2.34973 225.964 219.384
and
Initial parameters [0, 0, 0, -0.0650073, 1.4008, -2.19123]
versus
Initial parameters [0, 0, 0, -0.0650073, 1.4008, -2.19123]
Maybe a copy/paste error in your email ?
Question:
The raw images that you saved and
then converted to Analyze format,
are they the original DICOM series
that you are trying to register ?
or are they the result of the registration
performed on the DICOM images ?
Thanks
Luis
--------------------------------
Radhika Sivaramakrishna wrote:
> Hi Luis,
> Actually the images are 3D and are DICOM series.
> As a matter of fact, I do not get the same result.
> I get different results.
> I get the first output for center of rotation, when I run
> the registration directly on the DICOM series, however
> I get the second output for center of rotation when I run
> The same algorithm on the Analyze images.
> Hope this clarifies things.
> Thanks
> Radhika
>
>
> -----Original Message-----
> From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
> Sent: Thursday, January 15, 2004 10:58 AM
> To: Radhika Sivaramakrishna
> Cc: 'insight-users at itk.org'
> Subject: Re: [Insight-users] Image registration - 2 different
> initializations
>
>
> Hi Radhika,
>
> I didn't understand your question.
>
> According to your email, you are doing
> registration between two 2D images.
>
> When you read the images from DICOM format
> you get one registration result.
>
> and if you convert the DICOM to raw and
> then to Analyze format...
>
> then you get the *same* result.
>
>
> Why is this a bad thing ?
>
>
>
> Luis
>
>
>
> ------------------------------------
>
> Radhika Sivaramakrishna wrote:
>
> > Hi Luis,
> >
> > I appear to be having a strange problem with image registration.
> > Basically I am using the same code which you finally sent me although
> I have
> >
> > combined the previous code you sent me to read a dicom series so as to
> > directly read a pair of test-retest DICOM series. Since the data are
> > unsigned short
> >
> > there is already some problem I am having, I suspect w.r.t to
Endianness
> > which I have not solved. But I am getting some other strange things
> which
> >
> > I will try to describe below:
> >
> >
> >
> > When I directly run the registration code on the 2 dicom series, then
> I get
> >
> >
> >
> > Transform center before Initializer 0 0 0
> >
> > Transform center after Initializer -2.34973 225.964 219.384
> >
> > Intial Parameters =
> >
> > [0, 0, 0, -0.0650073, 1.4008, -2.19123]
> >
> > Translationscale = 1000
> >
> >
> >
> > However, when I save the images as Raw format and then convert that to
> > an Analyze file using ImageJ and then load in the two images again,
> > using the straight version
> >
> > of the code you sent me, here is what I get:
> >
> >
> >
> > Transform center before Initializer 0 0 0
> >
> > Transform center after Initializer -2.34973 225.964 219.384
> >
> > Intial Parameters =
> >
> > [0, 0, 0, -0.0650073, 1.4008, -2.19123]
> >
> > Translationscale = 1000
> >
> >
> >
> > I cant figure out what is going on. It appears the data is being read
> > fine, because the raw files for fixed and moving image are as they
> > should be when I view it on ImageJ.
> >
> >
> >
> > Can you help figure out what is happening.
> >
> >
> >
> > Thanks
> >
> > Radhika
> >
> >
> >
> > -----------------------------------------------------
> >
> > Confidentiality Notice.
> >
> > This email message is for the sole use of the intended recipient(s) and
> > may contain confidential and privileged information. Any unauthorized
> > review, use, disclosure or distribution is prohibited. If you are not
> > the intended recipient, please contact the sender by reply email and
> > destroy all copies of the original message. If you are the intended
> > recipient, please be advised that the content of this message is
subject
> > to access, review and disclosure by the sender's Email System
> Administrator.
> >
>
>
>
> -----------------------------------------------------
> Confidentiality Notice.
> This email message is for the sole use of the intended recipient(s) and
> may contain confidential and privileged information. Any unauthorized
> review, use, disclosure or distribution is prohibited. If you are not
> the intended recipient, please contact the sender by reply email and
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Administrator.
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5.5.2656.87">
<TITLE>RE: [Insight-users] Image registration - 2 different =
initializati ons</TITLE>
</HEAD>
<BODY>
<P><FONT SIZE=3D2>Hi Luis,</FONT>
<BR><FONT SIZE=3D2>I am really sorry about this. I think I pasted the =
wrong thing from my output.</FONT>
</P>
<P><FONT SIZE=3D2>Here it is with the DicomSeries -> Raw -> =
Analyze run:</FONT>
</P>
<P><FONT SIZE=3D2>Transform center before Initializer 0 0 =
0</FONT>
<BR><FONT SIZE=3D2> Transform center after Initializer =
123.619 150.723 97.2895</FONT>
<BR><FONT SIZE=3D2>Intial Parameters =3D</FONT>
<BR><FONT SIZE=3D2>[0, 0, 0, 0.661387, 1.31363, -0.631911]</FONT>
<BR><FONT SIZE=3D2> Translationscale =3D 1000</FONT>
</P>
<P><FONT SIZE=3D2>Here it is with the Dicom series run:</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>Transform center before Initializer 0 0 =
0</FONT>
<BR><FONT SIZE=3D2> Transform center after Initializer =
-2.34973 225.964 219.384</FONT>
<BR><FONT SIZE=3D2>Intial Parameters =3D</FONT>
<BR><FONT SIZE=3D2>[0, 0, 0, -0.0650073, 1.4008, -2.19123]</FONT>
<BR><FONT SIZE=3D2> Translationscale =3D 1000</FONT>
</P>
<P><FONT SIZE=3D2>Thanks</FONT>
<BR><FONT SIZE=3D2>Radhika</FONT>
</P>
<BR>
<BR>
<BR>
<BR>
<P><FONT SIZE=3D2>-----Original Message-----</FONT>
<BR><FONT SIZE=3D2>From: Luis Ibanez [<A =
HREF=3D"mailto:luis.ibanez at kitware.com">mailto:luis.ibanez at kitware.com</=
A>] </FONT>
<BR><FONT SIZE=3D2>Sent: Thursday, January 15, 2004 11:12 AM</FONT>
<BR><FONT SIZE=3D2>To: Radhika Sivaramakrishna</FONT>
<BR><FONT SIZE=3D2>Cc: 'insight-users at itk.org'</FONT>
<BR><FONT SIZE=3D2>Subject: Re: [Insight-users] Image registration - 2 =
different initializati ons</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>Hi Radhika,</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>Sorry... still unclear.</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>The two initialization values that you</FONT>
<BR><FONT SIZE=3D2>posted in your email look the same to me.</FONT>
<BR><FONT SIZE=3D2><A =
HREF=3D"http://www.itk.org/pipermail/insight-users/2004-January/006280.h=
tml" =
TARGET=3D"_blank">http://www.itk.org/pipermail/insight-users/2004-Januar=
y/006280.html</A></FONT>
</P>
<BR>
<P><FONT SIZE=3D2>Transform center after Initializer -2.34973 =
225.964 219.384</FONT>
</P>
<P><FONT =
SIZE=3D2> &nb=
sp; versus</FONT>
</P>
<P><FONT SIZE=3D2>Transform center after Initializer -2.34973 =
225.964 219.384</FONT>
</P>
<BR>
<P><FONT =
SIZE=3D2> &nb=
sp; and</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>Initial parameters [0, 0, 0, -0.0650073, 1.4008, =
-2.19123]</FONT>
</P>
<P><FONT =
SIZE=3D2> &nb=
sp; versus</FONT>
</P>
<P><FONT SIZE=3D2>Initial parameters [0, 0, 0, -0.0650073, 1.4008, =
-2.19123]</FONT>
</P>
<BR>
<BR>
<P><FONT SIZE=3D2>Maybe a copy/paste error in your email ?</FONT>
</P>
<BR>
<BR>
<BR>
<P><FONT SIZE=3D2>Question:</FONT>
</P>
<P><FONT SIZE=3D2> The raw images that you saved =
and</FONT>
<BR><FONT SIZE=3D2> then converted to Analyze =
format,</FONT>
<BR><FONT SIZE=3D2> are they the original DICOM =
series</FONT>
<BR><FONT SIZE=3D2> that you are trying to register =
?</FONT>
</P>
<P><FONT SIZE=3D2> or are they the result of the =
registration</FONT>
<BR><FONT SIZE=3D2> performed on the DICOM images =
?</FONT>
</P>
<BR>
<BR>
<BR>
<P><FONT SIZE=3D2>Thanks</FONT>
</P>
<BR>
<P><FONT SIZE=3D2> Luis</FONT>
</P>
<BR>
<BR>
<BR>
<P><FONT SIZE=3D2>--------------------------------</FONT>
<BR><FONT SIZE=3D2>Radhika Sivaramakrishna wrote:</FONT>
</P>
<P><FONT SIZE=3D2>> Hi Luis,</FONT>
<BR><FONT SIZE=3D2>> Actually the images are 3D and are DICOM =
series.</FONT>
<BR><FONT SIZE=3D2>> As a matter of fact, I do not get the same =
result.</FONT>
<BR><FONT SIZE=3D2>> I get different results.</FONT>
<BR><FONT SIZE=3D2>> I get the first output for center of rotation, =
when I run</FONT>
<BR><FONT SIZE=3D2>> the registration directly on the DICOM series, =
however</FONT>
<BR><FONT SIZE=3D2>> I get the second output for center of rotation =
when I run</FONT>
<BR><FONT SIZE=3D2>> The same algorithm on the Analyze =
images.</FONT>
<BR><FONT SIZE=3D2>> Hope this clarifies things.</FONT>
<BR><FONT SIZE=3D2>> Thanks</FONT>
<BR><FONT SIZE=3D2>> Radhika</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> -----Original Message-----</FONT>
<BR><FONT SIZE=3D2>> From: Luis Ibanez [<A =
HREF=3D"mailto:luis.ibanez at kitware.com">mailto:luis.ibanez at kitware.com</=
A>]</FONT>
<BR><FONT SIZE=3D2>> Sent: Thursday, January 15, 2004 10:58 =
AM</FONT>
<BR><FONT SIZE=3D2>> To: Radhika Sivaramakrishna</FONT>
<BR><FONT SIZE=3D2>> Cc: 'insight-users at itk.org'</FONT>
<BR><FONT SIZE=3D2>> Subject: Re: [Insight-users] Image registration =
- 2 different </FONT>
<BR><FONT SIZE=3D2>> initializations</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> Hi Radhika,</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> I didn't understand your question.</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> According to your email, you are doing</FONT>
<BR><FONT SIZE=3D2>> registration between two 2D images.</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> When you read the images from DICOM =
format</FONT>
<BR><FONT SIZE=3D2>> you get one registration result.</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> and if you convert the DICOM to raw and</FONT>
<BR><FONT SIZE=3D2>> then to Analyze format...</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> then you get the *same* =
result.</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> Why is this a bad thing ?</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> Luis</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> ------------------------------------</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> Radhika Sivaramakrishna wrote:</FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> > Hi Luis,</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > I appear to be having a strange =
problem with image registration.</FONT>
<BR><FONT SIZE=3D2>> > Basically I am using the same code =
which you finally sent me although </FONT>
<BR><FONT SIZE=3D2>> I have</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > combined the previous code you sent =
me to read a dicom series so as to</FONT>
<BR><FONT SIZE=3D2>> > directly read a pair of test-retest =
DICOM series. Since the data are</FONT>
<BR><FONT SIZE=3D2>> > unsigned short</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > there is already some problem I am =
having, I suspect w.r.t to Endianness</FONT>
<BR><FONT SIZE=3D2>> > which I have not solved. But I am =
getting some other strange things </FONT>
<BR><FONT SIZE=3D2>> which</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > I will try to describe below:</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > </FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > When I directly run the registration =
code on the 2 dicom series, then </FONT>
<BR><FONT SIZE=3D2>> I get</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > </FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Transform center before Initializer =
0 0 0</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Transform center after =
Initializer -2.34973 225.964 219.384</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Intial Parameters =3D</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > [0, 0, 0, -0.0650073, 1.4008, =
-2.19123]</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Translationscale =
=3D 1000</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > </FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > However, when I save the images as =
Raw format and then convert that to</FONT>
<BR><FONT SIZE=3D2>> > an Analyze file using ImageJ and =
then load in the two images again,</FONT>
<BR><FONT SIZE=3D2>> > using the straight version</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > of the code you sent me, here is =
what I get:</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > </FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Transform center before Initializer =
0 0 0</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Transform center after =
Initializer -2.34973 225.964 219.384</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Intial Parameters =3D</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > [0, 0, 0, -0.0650073, 1.4008, =
-2.19123]</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Translationscale =
=3D 1000</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > </FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > I cant figure out what is going on. =
It appears the data is being read</FONT>
<BR><FONT SIZE=3D2>> > fine, because the raw files for =
fixed and moving image are as they</FONT>
<BR><FONT SIZE=3D2>> > should be when I view it on =
ImageJ.</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > </FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Can you help figure out what is =
happening.</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > </FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Thanks</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Radhika</FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > </FONT>
<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > =
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<BR><FONT SIZE=3D2>> ></FONT>
<BR><FONT SIZE=3D2>> > Confidentiality Notice.</FONT>
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<BR><FONT SIZE=3D2>> > This email message is for the sole =
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<BR><FONT SIZE=3D2>> > may contain confidential and =
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