[Insight-users] Mystery solved
Radhika Sivaramakrishna
radhika.sivaramakrishna at synarc.com
Thu, 15 Jan 2004 12:56:23 -0800
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Hi Luis and Jim,
You were right. The spacing was correct, however origin had been
Reinitialized to 0 when I saved to Raw and this obviously remained when I
Converted to Analyze which explains the difference in center of rotation.
I found that the original DICOM series had an origin of:
Origin: -125.969 75.2403 122.094.
Thanks for helping sort this out.
Radhika
-----Original Message-----
From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
Sent: Thursday, January 15, 2004 11:50 AM
To: Radhika Sivaramakrishna
Cc: 'insight-users at itk.org'
Subject: Re: [Insight-users] Image registration - 2 different initializati
ons
Radhika,
When you converted the DICOM series to RAW and then
to Analyze format,.... how did you transferred the values
of image origin and image spacing ?
It is very likely that in the conversion process, the image
spacing was lost and the Analyze image got created with
a ficticious (anddangerous) spacing like 1.0 x 1.0 x 1.0.
Keep in mind that registration is performed in physical
units, not in pixels. If the image spacing information got
corrupted, the values of the initializer will be corrupted
as well.
You can easily check the image spacing by invoking
image->Print( std::cout );
or more specifically
std::cout << image->GetSpacing() << std::endl;
If you need to convert DICOM to Analyze you can
simply use MRIConvert (see previous email from
Jolinda Smith) or you can use the example program:
Insight/Examples/IO/
DicomSeriesReadImageWrite.cxx
They will keep the image origin and spacing
information.
Regards,
Luis
-----------------------------------
Radhika Sivaramakrishna wrote:
> 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
>
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<BR>
<P><FONT SIZE=3D2>Hi Luis and Jim,</FONT>
</P>
<P><FONT SIZE=3D2>You were right. The spacing was correct, however =
origin had been</FONT>
<BR><FONT SIZE=3D2>Reinitialized to 0 when I saved to Raw and this =
obviously remained when I</FONT>
<BR><FONT SIZE=3D2>Converted to Analyze which explains the difference =
in center of rotation.</FONT>
<BR><FONT SIZE=3D2>I found that the original DICOM series had an origin =
of:</FONT>
</P>
<P><FONT SIZE=3D2>Origin: -125.969 75.2403 122.094.</FONT>
</P>
<P><FONT SIZE=3D2>Thanks for helping sort this out.</FONT>
<BR><FONT SIZE=3D2>Radhika</FONT>
</P>
<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 11:50 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>Radhika,</FONT>
</P>
<P><FONT SIZE=3D2>When you converted the DICOM series to RAW and =
then</FONT>
<BR><FONT SIZE=3D2>to Analyze format,.... how did you transferred the =
values</FONT>
<BR><FONT SIZE=3D2>of image origin and image spacing ?</FONT>
</P>
<P><FONT SIZE=3D2>It is very likely that in the conversion process, the =
image</FONT>
<BR><FONT SIZE=3D2>spacing was lost and the Analyze image got created =
with</FONT>
<BR><FONT SIZE=3D2>a ficticious (anddangerous) spacing like 1.0 x =
1.0 x 1.0.</FONT>
</P>
<P><FONT SIZE=3D2>Keep in mind that registration is performed in =
physical</FONT>
<BR><FONT SIZE=3D2>units, not in pixels. If the image =
spacing information got</FONT>
<BR><FONT SIZE=3D2>corrupted, the values of the initializer will be =
corrupted</FONT>
<BR><FONT SIZE=3D2>as well.</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>You can easily check the image spacing by =
invoking</FONT>
</P>
<P><FONT =
SIZE=3D2> &nb=
sp; image->Print( =
std::cout );</FONT>
</P>
<P><FONT SIZE=3D2>or more specifically</FONT>
</P>
<P><FONT SIZE=3D2> =
std::cout << image->GetSpacing() << =
std::endl;</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>If you need to convert DICOM to Analyze you =
can</FONT>
<BR><FONT SIZE=3D2>simply use MRIConvert (see previous email =
from</FONT>
<BR><FONT SIZE=3D2>Jolinda Smith) or you can use the example =
program:</FONT>
</P>
<P><FONT SIZE=3D2> Insight/Examples/IO/</FONT>
<BR><FONT =
SIZE=3D2> &nb=
sp; =
DicomSeriesReadImageWrite.cxx</FONT>
<BR><FONT SIZE=3D2> </FONT>
<BR><FONT SIZE=3D2>They will keep the image origin and spacing</FONT>
<BR><FONT SIZE=3D2>information.</FONT>
</P>
<BR>
<BR>
<P><FONT SIZE=3D2>Regards,</FONT>
</P>
<BR>
<P><FONT SIZE=3D2> Luis</FONT>
</P>
<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>> I am really sorry about this. I think I pasted =
the wrong thing from my </FONT>
<BR><FONT SIZE=3D2>> output.</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> Here it is with the DicomSeries -> Raw -> =
Analyze run:</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><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>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> Here it is with the Dicom series run:</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>> 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>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> Thanks</FONT>
<BR><FONT SIZE=3D2>> Radhika</FONT>
<BR><FONT SIZE=3D2>></FONT>
</P>
<BR>
<P><FONT =
SIZE=3D2> &nb=
sp; &nb=
sp; &nb=
sp; &nb=
sp; </FONT>
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SIZE=3D2>----------------------------------------------------- =
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<BR><FONT SIZE=3D2>Confidentiality Notice. </FONT>
<BR><FONT SIZE=3D2>This email message is for the sole use of the =
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is prohibited. If you are not the intended recipient, please contact =
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