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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Bill</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks for the info and link to the
resampled data.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I am going to write myself a little script
to do option (2) from your list... so far I have been able to run the
resample example and both the series read/write example... now I will
attempt to combine all three into one file to resample the data to 1mm/pixel.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks again,</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Richard.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
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<p class=MsoNormal style='margin-left:36.0pt'><font size=2 face=Tahoma><span
lang=EN-US style='font-size:10.0pt;font-family:Tahoma'>-----Original
Message-----<br>
<b><span style='font-weight:bold'>From:</span></b> Bill Lorensen
[mailto:bill.lorensen@gmail.com] <br>
<b><span style='font-weight:bold'>Sent:</span></b> 28 February 2007 12:31<br>
<b><span style='font-weight:bold'>To:</span></b> Sims Richard (RKB) Clinical
Scientist<br>
<b><span style='font-weight:bold'>Cc:</span></b> insight-users@itk.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Insight-users]
Creating a 3D image with 2D images that exhibit variable image sp acing</span></font></p>
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<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Richard,</span></font></p>
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<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>ITK does not support
volumes with variable spacing. I have worked with the Visible Human data and
have handled this issue two ways:</span></font></p>
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face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
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<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>1) Create multiple 3D
volumes each with its own spacing.</span></font></p>
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<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>2) Resample each 3D
volume to a common spacing.</span></font></p>
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face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
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<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>I resampled the fresh CT
Visible Human Male and Female data sets into 1mm pixels and converted them to
DICOM. The University of Iowa hosts this data at:</span></font></p>
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<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><a
href="http://mri.radiology.uiowa.edu/VHDicom/index.html">http://mri.radiology.uiowa.edu/VHDicom/index.html</a></span></font></p>
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<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Bill<br>
<br>
</span></font></p>
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<p class=MsoNormal style='margin-left:36.0pt'><span class=gmailquote><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>On 2/28/07, <b><span
style='font-weight:bold'>Sims Richard (RKB) Clinical Scientist</span></b> <<a
href="mailto:Richard.Sims@uhcw.nhs.uk">Richard.Sims@uhcw.nhs.uk</a>> wrote:</span></font></span>
</p>
<div vlink=purple link=blue>
<div>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>Hi</span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>I'm wondering whether anyone can help me...</span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>...I have some visible human data of the head and
would like to create 3D volumes prior to performing a registration. The details
of the registration are not important at this stage, what I am more concerned
with is the finer details behind the 2D slices that create the volume. </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>One of the datasets (frozen CT) has a constant image
spacing for the 100 or so slices I am interested in (e.g. 0.55mm/pixel),
whereas the other dataset (normal, fresh CT) has variable image spacing ( e.g.
0.55-0.75mm/pixel). I have written a small matlab script to read in the *.txt
file that is provided with each 2D data file to create a separate *.mha file
that is then used with a script similar to the ImageSeriesReadWrite.cxx example
script to create a 3D dicom file. </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>When I check the header of the newly created 3D dicom
file there are only one pair of values for the image spacing, presumably of the
final image slice that was used to compile it. Does the newly created dicom
file contain the correct image spacing for all slices, or are they all stored
at the displayed value (therefore rendering the file useless)? </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>If this is the case, is there any way around it apart
from creating several smaller 3D dicom volumes?</span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>Many thanks in advance,</span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>Richard.</span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
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<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'> </span></font></p>
<p style='margin-left:36.0pt'><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>
</span></font></p>
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