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<div class=Section1>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Hi, Peter, Frank:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Thank you very much for your detailed explanations.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>This is the summary about what I understand now. Please let me know if I
made any mistake. Thank you very much!<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-spacerun:yes'> </span><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>There are three basic image classes that track image volume spatial information
in stack:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-tab-count:1'> </span><span
class=SpellE><span class=GramE>itkImagebase</span></span><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-tab-count:2'> </span>|<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-tab-count:1'> </span><span
class=SpellE><span class=GramE>itkImage</span></span><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-tab-count:2'> </span>|
<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-tab-count:1'> </span><span
class=SpellE><span class=GramE>itkOrientedImage</span></span><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-tab-count:2'> </span>|<span
style='mso-tab-count:1'> </span><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>They share the same class members:<span style='mso-tab-count:1'> </span><o:p></o:p></span></font></p>
<p class=MsoPlainText><span class=GramE><font size=2 face="Courier New"><span
style='font-size:10.0pt'>protected</span></font></span>:<o:p></o:p></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-spacerun:yes'> </span>/** Origin and spacing of
physical coordinates. <span class=GramE>This variables</span> are<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-spacerun:yes'> </span>* protected for
efficiency.<span style='mso-spacerun:yes'> </span>They are referenced
frequently by<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-spacerun:yes'> </span>* <span class=GramE>inner</span>
loop calculations. */<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-spacerun:yes'> </span><span class=SpellE><span
class=GramE>SpacingType</span></span><span class=GramE><span
style='mso-spacerun:yes'> </span><span class=SpellE>m</span></span><span
class=SpellE>_Spacing</span>;<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-spacerun:yes'> </span><span class=SpellE>PointType</span><span
style='mso-spacerun:yes'> </span><span class=SpellE>m_Origin</span>;<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><span style='mso-spacerun:yes'> </span><span class=SpellE>DirectionType</span>
<span class=SpellE>m_Direction</span>;<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>In 2.6.0, <span class=SpellE>itkImage</span> only works with images
that <span class=SpellE>m_Direction</span> = identity. And, thus, it shall be
used only for DICOM series with <span class=SpellE>Img-ori-pat</span> tag (0020|0037):
1\0\0\0\1\<span class=GramE>0,</span> provided that it shall be loaded into
stack from F to H.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>For all other cases, <span class=SpellE>itkOrientedImage</span> shall
be used.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>It seems very different from ITK SW Guide <span class=GramE>2.4,</span>
particularly <span class=SpellE>itkOrientedImage</span> class is not mentioned
in the guide. <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-Andrew <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>-----Original Message-----<br style='mso-special-character:line-break'>
<![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
<![endif]><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Message: 5<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Date: Fri, 14 Apr 2006 02:57:34 +0200<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>From: Peter Cech <pcech@vision.ee.ethz.ch><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Subject: Re: [Insight-users] 3D Image Volume Origin<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>To: insight-users@itk.org<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Message-ID: <20060414005734.GA25526@ee.ethz.ch><o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Content-Type: text/plain; charset=us-ascii<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>On Thu, Apr 13, 2006 at 11:57:01 -0700, Andrew Li wrote:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> Hi, ITK users:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> We are moving up ITK package from 2.4.0 to 2.6.0.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> There are some problems after ITK library is switched.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> Those problems seem related to the center of the 3D volume, which
is<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> related to Origin and Direction of the 3D volume.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> We just start to investigate the problems and we noticed that
there are<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> some changes made in IO/itkGDCMImageIO.cxx<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>In ITK 2.4.0
version: Date:<span style='mso-spacerun:yes'>
</span>$Date: 2005/11/29 21:58:28 $<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>// DICOM
specifies its origin in LPS coordinate, regardless of how<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>// the data is
acquired. itk's origin must be in the same<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>// coordinate
system as the data. This code transforms the DICOM<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>// origin into
the itk origin. The itk origin is computed by<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>// multiplying
the inverse(transpose) of the direction cosine times<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>// the dicom
origin.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'>
</span>vnl_vector<double> itkOrigin(3), dicomOrigin(3);<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'>
</span>vnl_matrix<double> dicomDirection(3,3);<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>dicomOrigin[0] =
header.GetXOrigin();<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>dicomOrigin[1] =
header.GetYOrigin();<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>dicomOrigin[2] =
header.GetZOrigin();<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>for (unsigned
int ii = 0; ii < 3; ii++)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>{<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'>
</span>dicomDirection[0][ii] = rowDirection[ii];<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'>
</span>dicomDirection[1][ii] = columnDirection[ii];<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'>
</span>dicomDirection[2][ii] = sliceDirection[ii];<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>}<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>itkOrigin =
dicomDirection * dicomOrigin;<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>m_Origin[0] =
itkOrigin[0];<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>m_Origin[1] =
itkOrigin[1];<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>m_Origin[2] =
itkOrigin[2];<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>While in ITK
2.6.0 version: Date:<span
style='mso-spacerun:yes'> </span>$Date:
2006/03/08 18:28:57 $<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>// Dicom's
origin is always in LPS<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>m_Origin[0] =
header.GetXOrigin();<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>m_Origin[1] =
header.GetYOrigin();<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>><span style='mso-spacerun:yes'> </span>m_Origin[2] =
header.GetZOrigin();<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> <o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> Could anyone tell us the reason of the changes and impact of the<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>> changes?<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>The problem is due to inconsistency between itkImage and<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>itkOrientedImage. itkImage is the original image type and assumes that<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Origin is in the same coordinate system as the image. In the ITK 2.2
new<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>image type itkOrientedImage
(http://www.itk.org/Wiki/Proposals:Orientation)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>was introduced and physical coordinate system was set to match that of<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>DICOM. Unlike itkImage, itkOrientedImage correctly computes physical<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>coordinates also with not axis-aligned volumes. I'm not completely sure<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>whether the physical coordinate system before this change was<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>unspecified or it was just assumed that all images were correctly<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>reoriented by user.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>The code in ITK 2.4 permuted the origin to match image orientation.
This<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>broke physical coordinates computation in itkOrientedImage and was<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>subsequently fixed. Unfortunately, now the itkImage won't give you<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>expected physical coordinates unless it is LPS oriented.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>For your current situation, I would suggest you switch from itkImage to<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>itkOrientedImage. It will solve your problem and as a bonus your<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>application will be able to correctly deal with non axis aligned<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>volumes.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Regards,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Peter Cech<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>**********************************<o:p></o:p></span></font></p>
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