[Insight-users] Image registration - 2 different initializati
ons
Miller, James V (Research)
millerjv at crd.ge.com
Thu, 15 Jan 2004 14:53:24 -0500
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Radhika,
For the case of taking DICOM->raw->Analyze, are you keeping track of the
pixel size and origin?
These "center" coordinates may be in physical coordinates. If you lost the
"origin" position when you converted to raw, then you may not be able to
relate the "centers".
Jim
-----Original Message-----
From: Radhika Sivaramakrishna [mailto:radhika.sivaramakrishna at synarc.com]
Sent: Thursday, January 15, 2004 2:17 PM
To: 'Luis Ibanez'
Cc: 'insight-users at itk.org'
Subject: RE: [Insight-users] Image registration - 2 different initializati
ons
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
<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
<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
<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
> 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.
>
-----------------------------------------------------
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<DIV><SPAN class=861035119-15012004><FONT color=#0000ff size=2>Radhika,
</FONT></SPAN></DIV>
<DIV><SPAN class=861035119-15012004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=861035119-15012004><FONT color=#0000ff size=2>For the case of
taking DICOM->raw->Analyze, are you keeping track of the pixel size and
origin?</FONT></SPAN></DIV>
<DIV><SPAN class=861035119-15012004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=861035119-15012004><FONT color=#0000ff size=2>These "center"
coordinates may be in physical coordinates. If you lost the "origin"
position when you converted to raw, then you may not be able to relate the
"centers".</FONT></SPAN></DIV>
<DIV><SPAN class=861035119-15012004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=861035119-15012004><FONT color=#0000ff
size=2>Jim</FONT></SPAN></DIV>
<BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> Radhika Sivaramakrishna
[mailto:radhika.sivaramakrishna at synarc.com]<BR><B>Sent:</B> Thursday, January
15, 2004 2:17 PM<BR><B>To:</B> 'Luis Ibanez'<BR><B>Cc:</B>
'insight-users at itk.org'<BR><B>Subject:</B> RE: [Insight-users] Image
registration - 2 different initializati ons<BR><BR></FONT></DIV>
<P><FONT size=2>Hi Luis,</FONT> <BR><FONT size=2>I am really sorry about this.
I think I pasted the wrong thing from my output.</FONT> </P>
<P><FONT size=2>Here it is with the DicomSeries -> Raw -> Analyze
run:</FONT> </P>
<P><FONT size=2>Transform center before Initializer 0 0 0</FONT>
<BR><FONT size=2> Transform center after Initializer 123.619
150.723 97.2895</FONT> <BR><FONT size=2>Intial Parameters =</FONT>
<BR><FONT size=2>[0, 0, 0, 0.661387, 1.31363, -0.631911]</FONT> <BR><FONT
size=2> Translationscale = 1000</FONT> </P>
<P><FONT size=2>Here it is with the Dicom series run:</FONT> </P><BR>
<P><FONT size=2>Transform center before Initializer 0 0 0</FONT>
<BR><FONT size=2> Transform center after Initializer -2.34973
225.964 219.384</FONT> <BR><FONT size=2>Intial Parameters =</FONT>
<BR><FONT size=2>[0, 0, 0, -0.0650073, 1.4008, -2.19123]</FONT> <BR><FONT
size=2> Translationscale = 1000</FONT> </P>
<P><FONT size=2>Thanks</FONT> <BR><FONT size=2>Radhika</FONT>
</P><BR><BR><BR><BR>
<P><FONT size=2>-----Original Message-----</FONT> <BR><FONT size=2>From: Luis
Ibanez [<A
href="mailto:luis.ibanez at kitware.com">mailto:luis.ibanez at kitware.com</A>]
</FONT><BR><FONT size=2>Sent: Thursday, January 15, 2004 11:12 AM</FONT>
<BR><FONT size=2>To: Radhika Sivaramakrishna</FONT> <BR><FONT size=2>Cc:
'insight-users at itk.org'</FONT> <BR><FONT size=2>Subject: Re: [Insight-users]
Image registration - 2 different initializati ons</FONT> </P><BR>
<P><FONT size=2>Hi Radhika,</FONT> </P><BR>
<P><FONT size=2>Sorry... still unclear.</FONT> </P><BR>
<P><FONT size=2>The two initialization values that you</FONT> <BR><FONT
size=2>posted in your email look the same to me.</FONT> <BR><FONT size=2><A
href="http://www.itk.org/pipermail/insight-users/2004-January/006280.html"
target=_blank>http://www.itk.org/pipermail/insight-users/2004-January/006280.html</A></FONT>
</P><BR>
<P><FONT size=2>Transform center after Initializer -2.34973
225.964 219.384</FONT> </P>
<P><FONT
size=2>
versus</FONT> </P>
<P><FONT size=2>Transform center after Initializer -2.34973
225.964 219.384</FONT> </P><BR>
<P><FONT
size=2>
and</FONT> </P><BR>
<P><FONT size=2>Initial parameters [0, 0, 0, -0.0650073, 1.4008,
-2.19123]</FONT> </P>
<P><FONT
size=2>
versus</FONT> </P>
<P><FONT size=2>Initial parameters [0, 0, 0, -0.0650073, 1.4008,
-2.19123]</FONT> </P><BR><BR>
<P><FONT size=2>Maybe a copy/paste error in your email ?</FONT>
</P><BR><BR><BR>
<P><FONT size=2>Question:</FONT> </P>
<P><FONT size=2> The raw images that you saved and</FONT>
<BR><FONT size=2> then converted to Analyze format,</FONT>
<BR><FONT size=2> are they the original DICOM series</FONT>
<BR><FONT size=2> that you are trying to register ?</FONT>
</P>
<P><FONT size=2> or are they the result of the
registration</FONT> <BR><FONT size=2> performed on the DICOM
images ?</FONT> </P><BR><BR><BR>
<P><FONT size=2>Thanks</FONT> </P><BR>
<P><FONT size=2> Luis</FONT> </P><BR><BR><BR>
<P><FONT size=2>--------------------------------</FONT> <BR><FONT
size=2>Radhika Sivaramakrishna wrote:</FONT> </P>
<P><FONT size=2>> Hi Luis,</FONT> <BR><FONT size=2>> Actually the images
are 3D and are DICOM series.</FONT> <BR><FONT size=2>> As a matter of fact,
I do not get the same result.</FONT> <BR><FONT size=2>> I get different
results.</FONT> <BR><FONT size=2>> I get the first output for center of
rotation, when I run</FONT> <BR><FONT size=2>> the registration directly on
the DICOM series, however</FONT> <BR><FONT size=2>> I get the second output
for center of rotation when I run</FONT> <BR><FONT size=2>> The same
algorithm on the Analyze images.</FONT> <BR><FONT size=2>> Hope this
clarifies things.</FONT> <BR><FONT size=2>> Thanks</FONT> <BR><FONT
size=2>> Radhika</FONT> <BR><FONT size=2>> </FONT><BR><FONT size=2>>
</FONT><BR><FONT size=2>> -----Original Message-----</FONT> <BR><FONT
size=2>> From: Luis Ibanez [<A
href="mailto:luis.ibanez at kitware.com">mailto:luis.ibanez at kitware.com</A>]</FONT>
<BR><FONT size=2>> Sent: Thursday, January 15, 2004 10:58 AM</FONT>
<BR><FONT size=2>> To: Radhika Sivaramakrishna</FONT> <BR><FONT size=2>>
Cc: 'insight-users at itk.org'</FONT> <BR><FONT size=2>> Subject: Re:
[Insight-users] Image registration - 2 different </FONT><BR><FONT size=2>>
initializations</FONT> <BR><FONT size=2>> </FONT><BR><FONT size=2>>
</FONT><BR><FONT size=2>> Hi Radhika,</FONT> <BR><FONT size=2>>
</FONT><BR><FONT size=2>> I didn't understand your question.</FONT>
<BR><FONT size=2>> </FONT><BR><FONT size=2>> According to your email,
you are doing</FONT> <BR><FONT size=2>> registration between two 2D
images.</FONT> <BR><FONT size=2>> </FONT><BR><FONT size=2>> When you
read the images from DICOM format</FONT> <BR><FONT size=2>> you get one
registration result.</FONT> <BR><FONT size=2>> </FONT><BR><FONT size=2>>
and if you convert the DICOM to raw and</FONT> <BR><FONT size=2>> then to
Analyze format...</FONT> <BR><FONT size=2>> </FONT><BR><FONT
size=2>> then you get the *same* result.</FONT>
<BR><FONT size=2>> </FONT><BR><FONT size=2>> </FONT><BR><FONT
size=2>> Why is this a bad thing ?</FONT> <BR><FONT size=2>>
</FONT><BR><FONT size=2>> </FONT><BR><FONT size=2>> </FONT><BR><FONT
size=2>> Luis</FONT> <BR><FONT size=2>>
</FONT><BR><FONT size=2>> </FONT><BR><FONT size=2>> </FONT><BR><FONT
size=2>> ------------------------------------</FONT> <BR><FONT size=2>>
</FONT><BR><FONT size=2>> Radhika Sivaramakrishna wrote:</FONT> <BR><FONT
size=2>> </FONT><BR><FONT size=2>> > Hi Luis,</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > I appear to be
having a strange problem with image registration.</FONT> <BR><FONT
size=2>> > Basically I am using the same code which you finally
sent me although </FONT><BR><FONT size=2>> I have</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > combined the
previous code you sent me to read a dicom series so as to</FONT> <BR><FONT
size=2>> > directly read a pair of test-retest DICOM series. Since
the data are</FONT> <BR><FONT size=2>> > unsigned short</FONT>
<BR><FONT size=2>> ></FONT> <BR><FONT size=2>> > there
is already some problem I am having, I suspect w.r.t to Endianness</FONT>
<BR><FONT size=2>> > which I have not solved. But I am getting
some other strange things </FONT><BR><FONT size=2>> which</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > I will try to
describe below:</FONT> <BR><FONT size=2>> ></FONT> <BR><FONT
size=2>> > </FONT><BR><FONT size=2>> ></FONT>
<BR><FONT size=2>> > When I directly run the registration code on
the 2 dicom series, then </FONT><BR><FONT size=2>> I get</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> >
</FONT><BR><FONT size=2>> ></FONT> <BR><FONT size=2>>
> Transform center before Initializer 0 0 0</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > Transform
center after Initializer -2.34973 225.964 219.384</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > Intial
Parameters =</FONT> <BR><FONT size=2>> ></FONT> <BR><FONT
size=2>> > [0, 0, 0, -0.0650073, 1.4008, -2.19123]</FONT>
<BR><FONT size=2>> ></FONT> <BR><FONT size=2>> >
Translationscale = 1000</FONT> <BR><FONT size=2>>
></FONT> <BR><FONT size=2>> > </FONT><BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > However, when I
save the images as Raw format and then convert that to</FONT> <BR><FONT
size=2>> > an Analyze file using ImageJ and then load in the two
images again,</FONT> <BR><FONT size=2>> > using the straight
version</FONT> <BR><FONT size=2>> ></FONT> <BR><FONT
size=2>> > of the code you sent me, here is what I get:</FONT>
<BR><FONT size=2>> ></FONT> <BR><FONT size=2>> >
</FONT><BR><FONT size=2>> ></FONT> <BR><FONT size=2>>
> Transform center before Initializer 0 0 0</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > Transform
center after Initializer -2.34973 225.964 219.384</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > Intial
Parameters =</FONT> <BR><FONT size=2>> ></FONT> <BR><FONT
size=2>> > [0, 0, 0, -0.0650073, 1.4008, -2.19123]</FONT>
<BR><FONT size=2>> ></FONT> <BR><FONT size=2>> >
Translationscale = 1000</FONT> <BR><FONT size=2>>
></FONT> <BR><FONT size=2>> > </FONT><BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > I cant figure
out what is going on. It appears the data is being read</FONT> <BR><FONT
size=2>> > fine, because the raw files for fixed and moving image
are as they</FONT> <BR><FONT size=2>> > should be when I view it
on ImageJ.</FONT> <BR><FONT size=2>> ></FONT> <BR><FONT
size=2>> > </FONT><BR><FONT size=2>> ></FONT>
<BR><FONT size=2>> > Can you help figure out what is
happening.</FONT> <BR><FONT size=2>> ></FONT> <BR><FONT
size=2>> > </FONT><BR><FONT size=2>> ></FONT>
<BR><FONT size=2>> > Thanks</FONT> <BR><FONT size=2>>
></FONT> <BR><FONT size=2>> > Radhika</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> >
</FONT><BR><FONT size=2>> ></FONT> <BR><FONT size=2>>
> -----------------------------------------------------</FONT> <BR><FONT
size=2>> ></FONT> <BR><FONT size=2>> > Confidentiality
Notice.</FONT> <BR><FONT size=2>> ></FONT> <BR><FONT
size=2>> > This email message is for the sole use of the intended
recipient(s) and</FONT> <BR><FONT size=2>> > may contain
confidential and privileged information. Any unauthorized</FONT> <BR><FONT
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If you are not</FONT> <BR><FONT size=2>> > the intended recipient,
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