<div dir="ltr"><div><div><div>Hi Simon,<br><br></div>thank you for your code. Unfortunately, I can not work on this any longer. I hope it will be useful for someone else.<br><br></div>Cheers,<br></div>MG<br></div><div class="gmail_extra"><br><div class="gmail_quote">2016-02-05 9:32 GMT-05:00 Simon Rit <span dir="ltr"><<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi MG,<br>
Sorry, I realized I said something stupid. Using tif or mha won't
make any difference because there is a branching on the pixel type
in the <a href="http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html" target="_blank">projectionsreader</a>
(search for ushort in the graph of the <a href="http://www.openrtk.org/Doxygen/classrtk_1_1ProjectionsReader.html" target="_blank">doxygen
doc</a>) and unsigned short are handled differently. <br>
The enclosed pyhon code will reproduce the same as my previous
command line application. The commented code in it is what I
initially used to read projections without any processing, i.e.,
assuming line integrals.<br>
I still think there is a problem in the geometry but someone (you?)
has to spend sometime trying to understand what are the parameters
from the Matlab code.<br>
Keep us posted and good luck,<br>
Simon<div><div class="h5"><br>
<br>
<div>On 28/01/2016 22:27, MG Vallet wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Louie,
<div>I played with sdd and sid, following your advise. But they
have few effect, clearly less effect than proj_iso_x. And none
of these parameters can significantly improve my result. </div>
<div><br>
</div>
<div>Simon,</div>
<div>I carefully checked every input data and I cant see what I
did wrong. I want first to reproduce your output. You said
earlier it's easy to convert a series of tiff image into a mha
file using SimpleRTK. Do you mean by writing a short program,
or is it possible from the command line ? </div>
<div><br>
</div>
<div>MG</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2016-01-26 17:17 GMT-05:00 louie L <span dir="ltr"><<a href="mailto:ghostcz@hotmail.com" target="_blank">ghostcz@hotmail.com</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div link="blue" vlink="#954F72" lang="EN-US">
<div>
<p class="MsoNormal">Hi MG,</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Sometimes, the progressive
deformation from the center of rotation to the edge of
the image is caused by wrong sdd/sid ratio. Such as
change in the geometry will lead to distortion of the
image and wrong magnification.</p>
<p class="MsoNormal">Maybe you can play with that
parameter and report your result. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Cheers,</p>
<p class="MsoNormal">Louie</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Sent from <a href="http://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p>
<p class="MsoNormal"><span> </span></p>
<div style="border:none;border-top:solid #e1e1e1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="border:none;padding:0in"><br>
<b>From: </b><a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">Simon Rit</a><br>
<b>Sent: </b>Tuesday, January 26, 2016 13:24<br>
<b>To: </b><a href="mailto:mgvallet.pro@gmail.com" target="_blank">MG Vallet</a><br>
<b>Cc: </b><a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a><br>
<b>Subject: </b>Re: [Rtk-users] Sophia beads
reconstruction</p>
</div>
<div>
<div>
<p class="MsoNormal"><span> </span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span>Hi,</span><span></span></p>
</div>
<p class="MsoNormal"><span>I think it's likely a
problem with parameters. The best would be
to obtain them from the Matlab code they
provide.</span></p>
</div>
<div>
<p class="MsoNormal"><span>Good luck,</span></p>
</div>
<p class="MsoNormal"><span>Simon</span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span>On Mon, Jan 25, 2016
at 5:48 PM, MG Vallet <<a href="mailto:mgvallet.pro@gmail.com" target="_blank"></a><a href="mailto:mgvallet.pro@gmail.com" target="_blank">mgvallet.pro@gmail.com</a>>
wrote:</span></p>
</div>
</div>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal"><span>Hi Simon,</span></p>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>this was a
point I missed. I had to do the log
mapping.</span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>I must say, I
do not use RTK from shell. I just
plugged the objects</span></p>
</div>
<div>
<p class="MsoNormal"><span>FDKConeBeamReconstructionFilter
and ThreeDCircularProjectionGeometry
from RTK into a visualisation
software. That's the reason I'm not
absolutely sure about the length
parameter setting.</span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>Anyway, I'm now
pretty close to your result. I believe
the only difference is the progressive
deformation of beads with the distance
to center.</span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>What's your
opinion : is there another step I
might have missed, or is it more
likely a problem with parameters ?</span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>MG</span></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span> </span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span>2016-01-21
14:22 GMT-05:00 Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank"></a><a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>:</span></p>
</div>
</div>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal"><span>Not
exactly.
rtk::FDKConeBeamProjectionFilter
assumes that you pass the line
integral (ln(I0/I)). But
rtkfdk uses the
ProjectionsReader to read the
projections and converts them
depending on the type: for mha
or mhd, it just reads it and
nothing else. For tif, it
assumes that I is passed, try
to guess I0 (or gets it from
the cmd line) and computes
ln(I0/I).<br>
So from each tif projection,
instead of letting them go
through the ProjectionsReader
in RTK, directly use the
ImageReader, stack them and
pass it to the reconstruction
algorithm. In other words, if
you use SimpleRTK, use
ImageSeriesReader instead of
ProjectionsReader.<br>
Regarding the geometry, it
would be nice to be confident
in the geometry parameters,
maybe from their Matlab code?<span style="color:#888888"><br>
Simon</span></span></p>
</div>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span> </span></p>
<div>
<p class="MsoNormal"><span>On
21/01/2016 20:02, MG
Vallet wrote:</span></p>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<p class="MsoNormal"><span>Hi
Simon and Cyril, </span></p>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>I
really appreciate
your insight.</span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>By
examining the
parameters of the
acquisition, I saw
that the center must
effectively be
offset (4.8 mm in
both directions).
For the attached
image, I also
increases sdd and
sid by a factor
1000, just in case I
would be wrong in
units. It reduces
the first default I
pointed out in my
first message. Also
note that my input
dataset was </span><span>SophiaBeads_512_averaged.</span><span></span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>Regarding
the
pre-processing mentioned by
Simon, I need more
help. Is it as
simple as the FDK
filter assumes that
the input is
intensity, but the
dataset provides
-ln(I/I0) ?</span><span></span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>Regards,</span><span></span></p>
</div>
<div>
<p class="MsoNormal"><span>mg</span><span></span></p>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span>2016-01-20
3:33 GMT-05:00 Simon
Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank"></a><a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>>:</span></p>
</div>
</div>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><span>Hi,</span></p>
</div>
<p class="MsoNormal"><span>I
quickly
checked
SophiaBeads_64_averaged.zip.
First, it
seems that
what is
provided is
directly the
line integral.
RTK will
process the
tif images as
if it were a
photon count
so I converted
the tif
projections to
mha to avoid
this. For the
conversion, I
used another
piece of
software but
you can easily
do the same
thing with
SimpleRTK.</span></p>
</div>
<p class="MsoNormal"><span>Second,
I used the
enclosed
script which
gives me a
much better
result. I have
however a
geometry
problem. I
think they
provide a
Matlab piece
of code to get
the center of
rotation. If
you can run it
and find out
what is this
center, then
you can use it
to configure
the geometry
better with
the options
--proj_iso_x
and
--proj_iso_y.</span></p>
</div>
<p class="MsoNormal"><span>Good
luck,</span></p>
</div>
<p class="MsoNormal"><span>Simon</span></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span> </span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span>On
Tue, Jan 19,
2016 at 8:02
PM, MG Vallet
<<a href="mailto:mgvallet.pro@gmail.com" target="_blank"></a><a href="mailto:mgvallet.pro@gmail.com" target="_blank">mgvallet.pro@gmail.com</a>>
wrote:</span></p>
</div>
</div>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal"><span>Thanks
Cyril! </span></p>
<div>
<p class="MsoNormal"><span>going
to carefully
check my
inputs and I
give you some
news.</span></p>
</div>
<div>
<p class="MsoNormal"><span>mgv</span></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><span> </span></p>
<div>
<div>
<div>
<p class="MsoNormal"><span>2016-01-19
10:33
GMT-05:00
Cyril Mory
<<a href="mailto:cyril.mory@uclouvain.be" target="_blank"></a><a href="mailto:cyril.mory@uclouvain.be" target="_blank">cyril.mory@uclouvain.be</a>>:</span></p>
</div>
</div>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<div>
<p class="MsoNormal"><span>Hi,
<br>
<br>
It looks like
the geometry
is wrong
indeed,
because I have
never seen
such
artifacts.<br>
<br>
Hope that
helps,<br>
Cyril </span></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span> </span></p>
<div>
<p class="MsoNormal"><span>Le
19/01/2016
16:19, MG
Vallet a
écrit :</span></p>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<p class="MsoNormal"><span>Dear
rtk-users, </span></p>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span>I
applied the </span><span>FDKConeBeamReconstructionFilter to a data set
from </span><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#333333"><a href="https://zenodo.org/record/16539" target="_blank"></a><a href="https://zenodo.org/record/16539" target="_blank">https://zenodo.org/record/16539</a>. </span><span></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333">This
is a plastic
tube filled
with glass
beads that has
been scanned.</span><span></span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333">Attached
is a view of
the
reconstructed
central slice.
It is found
that:</span><span></span></p>
</div>
<div>
<ol start="1" type="1">
<li class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333">the
beads are
quickly
deformed
outside the
center</span><span></span></li>
<li class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333">each
one has a
halo, or a
shadow (dont
know the
proper term)</span><span></span></li>
</ol>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333">My
question is if
these are
simply
expected
artifacts. I
am not 100%
sure I
properly set
the geometry
parameters.</span><span></span></p>
</div>
<div>
<p class="MsoNormal"><span> </span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333">Regards,</span><span></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:#333333">mgv</span><span></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span> </span></p>
</div>
</div>
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par le
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