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Dear Uffe,<br>
<br>
Simply increasing the size of the reconstructed volume until the
object is fully contained in it should do the trick. An intuitive
way to understand this is the following: the algorithm tries to
"explain" the attenuation it sees on the projections. If the data
has been partially truncated, some rays have "extra attenuation"
that has to go somewhere in the reconstructed volume. The center of
the reconstructed volume is constrained by all the other rays, so
this "extra attenuation" is pushed to the borders. If, on the other
hand, the reconstructed volume is large enough, this "extra
attenuation" can go where it belongs, and does not cause
hyperattenuation on the borders.<br>
<br>
Note that you can still apply a crop to FOV at the very end of the
reconstruction process.<br>
<br>
I hope it helps<br>
Regards,<br>
Cyril<br>
<br>
<div class="moz-cite-prefix">On 06/19/2014 11:02 AM, Uffe Bernchou
wrote:<br>
</div>
<blockquote
cite="mid:C1D121D59E5C7040947FEC5D6B42942C10327A1E@SRVODEEXCH04.Rsyd.net"
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<div class="Section1">
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Dear Cyril,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size:
10.0pt;font-family:Arial;color:navy"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB">We are currently playing with the 3D
TV regularization iterative reconstruction
implemented in RTK for our cone beam data. The
results look promising indeed.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB">One thing that worries me a little is
a ring artefact we observe in the reconstructions
(please see attached image). This ring artefact we
usually remove in the standard fdk reconstruction
by using padding. Does the TV regularization
iterative reconstruction have a similar feature
for removing the ring artefact? <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB">Best regards<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB">Uffe Bernchou<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"><o:p> </o:p></span></font></p>
<div>
<div class="MsoNormal" style="text-align:center"
align="center"><font color="black" face="Times New
Roman" size="3"><span
style="font-size:12.0pt;color:windowtext">
<hr tabindex="-1" align="center" size="2"
width="100%">
</span></font></div>
<p class="MsoNormal"><b><font color="black"
face="Tahoma" size="2"><span
style="font-size:10.0pt;font-family:Tahoma;color:windowtext;font-weight:bold"
lang="EN-GB">Fra:</span></font></b><font
color="black" face="Tahoma" size="2"><span
style="font-size:10.0pt;
font-family:Tahoma;color:windowtext"
lang="EN-GB"> Cyril Mory
[<a class="moz-txt-link-freetext" href="mailto:cyril.mory@creatis.insa-lyon.fr">mailto:cyril.mory@creatis.insa-lyon.fr</a>] <br>
<b><span style="font-weight:bold">Sendt:</span></b>
3. juni 2014 17:30<br>
<b><span style="font-weight:bold">Til:</span></b>
Uffe Berncho</span></font><font color="black"
face="Tahoma" size="2"><span
style="font-size:10.0pt;font-family:Tahoma;
color:windowtext">u;
<st1:personname w:st="on">'Simon Rit'</st1:personname><br>
<b><span style="font-weight:bold">Cc:</span></b>
<st1:personname w:st="on"><a class="moz-txt-link-abbreviated" href="mailto:rtk-users@openrtk.org">rtk-users@openrtk.org</a></st1:personname><br>
<b><span style="font-weight:bold">Emne:</span></b>
Re: [Rtk-users] Release of RTK v1.0.0</span></font><font
color="black"><span style="color:windowtext"><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times New
Roman" size="3"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New
Roman" size="3"><span style="font-size:12.0pt">Dear
Uffe,<br>
<br>
The method is described and compared to others in
this PhD thesis :<br>
<a moz-do-not-send="true"
href="http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf">http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf</a><br>
That's for the pdf. You can access the description
here : <br>
<a moz-do-not-send="true"
href="http://tel.archives-ouvertes.fr/tel-00985728">http://tel.archives-ouvertes.fr/tel-00985728</a><br>
<br>
Your comments/questions are welcome.<br>
<br>
Best regards,<br>
Cyril<o:p></o:p></span></font></p>
<div>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="3"><span style="font-size:12.0pt">Le
03/06/2014 14:36, Uffe Bernchou a écrit :<o:p></o:p></span></font></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"
cite="mid:C1D121D59E5C7040947FEC5D6B42942C10316FF3@SRVODEEXCH04.Rsyd.net"
type="cite">
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Dear Simon,<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span style="font-size:
10.0pt;font-family:Arial;color:navy"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB">Do you have a reference publication
for the new iterative 3D reconstruction with 3D
TV regularization implemented in the v.1.00
release of RTK?<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB">Best regards,<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB">Uffe<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"><u1:p> </u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt"
lang="EN-GB">------------------------------<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt"
lang="EN-GB">Uffe Bernchou, Ph.D.<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt"
lang="EN-GB">Postdoc<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt"
lang="EN-GB"> <u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt"
lang="EN-GB">Laboratory of Radiation Physics,
<st1:place w:st="on"><st1:placename w:st="on">Odense</st1:placename>
<st1:placetype w:st="on">
University</st1:placetype> <st1:placetype
w:st="on">Hospital<u1:p></u1:p></st1:placetype></st1:place></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt"
lang="EN-GB">Institute of Clinical Research,
<st1:place w:st="on"><st1:placetype w:st="on">University</st1:placetype>
of <st1:placename w:st="on">
Southern Denmark<u1:p></u1:p></st1:placename></st1:place></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt"
lang="EN-GB">Email:
</span></font><font size="2"><span
style="font-size:10.0pt"><a
href="mailto:uffe.bernchou@rsyd.dk"
title="mailto:uffe.bernchou@rsyd.dk"
moz-do-not-send="true"><span lang="EN-GB">uffe.bernchou@rsyd.dk</span></a></span></font><o:p></o:p></p>
<u1:p></u1:p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt"
lang="EN-GB">Phone: +45 29796478<u1:p></u1:p></span></font><o:p></o:p></p>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="2"><span style="font-size:10.0pt">Sdr.
Boulevard 29, Indgang 97, 5000 Odense C</span></font><o:p></o:p></p>
<u1:p></u1:p>
<p class="MsoNormal"><font color="navy" face="Arial"
size="2"><span
style="font-size:10.0pt;font-family:Arial;color:navy"
lang="EN-GB"><u1:p> </u1:p></span></font><o:p></o:p></p>
<div>
<div class="MsoNormal" style="text-align:center"
align="center"><font color="black" face="Times New
Roman" size="3"><span style="font-size:12.0pt">
<hr tabindex="-1" align="center" size="2"
width="100%">
</span></font></div>
<p class="MsoNormal"><b><font color="black"
face="Tahoma" size="2"><span
style="font-size:10.0pt;font-family:Tahoma;font-weight:bold">Fra:</span></font></b><font
face="Tahoma" size="2"><span
style="font-size:10.0pt;font-family:Tahoma">
Rtk-users [<a moz-do-not-send="true"
href="mailto:rtk-users-bounces@openrtk.org">mailto:rtk-users-bounces@openrtk.org</a>]
<b><span style="font-weight:bold">På vegne af
</span></b>Simon Rit<br>
<b><span style="font-weight:bold">Sendt:</span></b>
28. april 2014 16:33<br>
<b><span style="font-weight:bold">Til:</span></b>
<a moz-do-not-send="true"
href="mailto:rtk-users@openrtk.org">
rtk-users@openrtk.org</a><br>
<b><span style="font-weight:bold">Emne:</span></b>
[Rtk-users] Release of RTK v1.0.0</span></font><u1:p></u1:p><o:p></o:p></p>
</div>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="3"><span style="font-size:12.0pt"><u1:p> </u1:p><o:p></o:p></span></font></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><font
color="black"
face="Times
" size="3"><span
style="font-size:12.0pt;font-family:"Times\000D\000A"">Dear
RTK users,<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><font
color="black"
face="Times
" size="3"><span
style="font-size:12.0pt;font-family:"Times\000D\000A"">It
is my pleasure to
announce the release
of RTK v1.0.0. As
announced previously
on the mailing list,
the new release is no
more compatible with
ITK 3.20, this release
is compatible with ITK
v4.2.0 and more recent
releases. We are still
actively developing
RTK with both new
filtered
backprojection and
iterative algorithms
so I still encourage
the use of git to be
up-to-date. As usual,
please report any
issue that you
encounter with RTK, we
are happy to help when
we can. Note the l<a
href="http://www.openrtk.org/RTK/project/publications.php"
target="_blank"
moz-do-not-send="true">ist
of publications
using RTK</a> on the
main site: please send
me the DOI of your
articles if you want
them to appear there.
We have also added a
webpage with
<a
href="http://www.openrtk.org/RTK/project/casestudies.html"
target="_blank"
moz-do-not-send="true">
use cases</a>.<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><font
color="black"
face="Times
" size="3"><span
style="font-size:12.0pt;font-family:"Times\000D\000A"">I'm
looking forward to
your feedback.
Regards,<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><font
color="black"
face="Times
" size="3"><span
style="font-size:12.0pt;font-family:"Times\000D\000A"">Simon<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><font
color="black"
face="Times
" size="3"><span
style="font-size:12.0pt;font-family:"Times\000D\000A""><br>
Release notes:<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<p class="MsoNormal"><font
color="black" face="Times
" size="3"><span
style="font-size:12.0pt;font-family:"Times\000D\000A"">-
introduction of the
itk::CudaImage object
that better handles the
memory transfers between
the CPU and the GPU<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<p class="MsoNormal"><font
color="black" face="Times
New
" size="3"><span
style="font-size:12.0pt;font-family:"Times
New\000D\000A"">-
pre-processing for
projection images:
binning, median filter,
lookup-table filter<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<p class="MsoNormal"><font
color="black" face="Times New
" size="3"><span
style="font-size:12.0pt;font-family:"Times
New\000D\000A"">-
filtered backprojection with
offset center-of-rotation
based on [Gullberg et al,
TMI, 1986]<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><font
color="black" face="Times New
" size="3"><span
style="font-size:12.0pt;font-family:"Times
New\000D\000A"">-
improved Joseph forward
projector and implementation
of its exact adjoint<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<p class="MsoNormal"><font
color="black" face="Times New
" size="3"><span
style="font-size:12.0pt;font-family:"Times
New\000D\000A"">-
improved SART reconstruction
[Andersen, Ultrason Imaging,
1984]<br>
- new iterative 3D
reconstruction using conjugate
gradient optimization<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"
style="margin-bottom:12.0pt"><font
color="black" face="Times New Roman"
size="3"><span
style="font-size:12.0pt">- new
iterative 3D reconstruction with
3D TV regularization using the
Alternating Direction Method of
Multipliers combined with the
Augmented Lagrangian method<u1:p></u1:p><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black"
face="Times New Roman" size="3"><span
style="font-size:12.0pt">Documentation:<u1:p></u1:p><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black"
face="Times New Roman" size="3"><span
style="font-size:12.0pt">- improved
Doxygen with dot graphs to describe
mini-pipelines, e.g., in the
<a
href="http://www.openrtk.org/Doxygen/classrtk_1_1SARTConeBeamReconstructionFilter.html"
target="_blank"
moz-do-not-send="true">
SART page</a><u1:p></u1:p><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black"
face="Times New Roman" size="3"><span
style="font-size:12.0pt">- updated
<a
href="http://www.openrtk.org/RTK/project/consortium.html"
target="_blank" moz-do-not-send="true">
consortium</a> and <a
href="http://www.openrtk.org/RTK/resources/alternatives.html"
target="_blank" moz-do-not-send="true">
alternative platforms</a> pages<u1:p></u1:p><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black"
face="Times New Roman" size="3"><span
style="font-size:12.0pt">- updated wiki<u1:p></u1:p><o:p></o:p></span></font></p>
</div>
</div>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="3"><span
style="font-size:12.0pt"><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font color="black" face="Times
New Roman" size="3"><span style="font-size:12.0pt"><br>
<br>
<br>
</span></font></p>
<font color="black" face="Times New Roman" size="3">
<fieldset class="mimeAttachmentHeader"></fieldset>
<o:p></o:p></font>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">_______________________________________________<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">Rtk-users mailing list<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt"><a moz-do-not-send="true" href="mailto:Rtk-users@openrtk.org">Rtk-users@openrtk.org</a><o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt"><a moz-do-not-send="true" href="http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users">http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users</a><o:p></o:p></span></font></pre>
</blockquote>
<p class="MsoNormal"><font color="black" face="Times New
Roman" size="3"><span style="font-size:12.0pt"><br>
<br>
<o:p></o:p></span></font></p>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">-- <o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">Cyril Mory, Post-doc<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">CREATIS<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">Leon Berard cancer treatment center<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">28 rue Laënnec<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">69373 Lyon cedex 08 FRANCE<o:p></o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt"><o:p> </o:p></span></font></pre>
<pre><font color="black" face="Courier New" size="2"><span style="font-size:10.0pt">Mobile: +33 6 69 46 73 79<o:p></o:p></span></font></pre>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font
color="black" face="Times New Roman" size="3"><span
style="font-size:12.0pt"><o:p> </o:p></span></font></p>
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align="center"><font color="black" face="Times New
Roman" size="3"><span style="font-size:12.0pt">
<hr align="center" color="#909090"
noshade="noshade" size="1" width="99%">
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style="border-collapse:collapse" border="0"
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<p class="MsoNormal"><font color="black"
face="Times New Roman" size="3"><span
style="font-size:12.0pt"><a
moz-do-not-send="true"
href="http://www.avast.com/"><span
style="text-decoration:none"><img
moz-do-not-send="true"
id="_x0000_i1027"
src="http://static.avast.com/emails/avast-mail-stamp.png"
border="0" height="33" width="90"></span></a><o:p></o:p></span></font></p>
</td>
<td style="padding:.75pt .75pt .75pt .75pt">
<p><font color="#3d4d5a" face="Calibri" size="3"><span
style="font-size:12.0pt;
font-family:Calibri;color:#3D4D5A">Ce
courrier électronique ne contient aucun
virus ou logiciel malveillant parce que
<st1:personname productid="la protection
Antivirus"
w:st="on">
la protection <a moz-do-not-send="true"
href="http://www.avast.com/">Antivirus
avast!</a> est active. <o:p>
</o:p></st1:personname></span></font></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"><font color="black" face="Times New
Roman" size="3"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
</div>
</o:smarttagtype></o:smarttagtype></o:smarttagtype></o:smarttagtype></blockquote>
<br>
<pre class="moz-signature" cols="72">--
--
Cyril Mory, Post-doc
CREATIS
Leon Berard cancer treatment center
28 rue Laënnec
69373 Lyon cedex 08 FRANCE
Mobile: +33 6 69 46 73 79</pre>
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