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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?<br>
Simon<br>
<br>
<div class="moz-cite-prefix">On 21/01/2016 20:02, MG Vallet wrote:<br>
</div>
<blockquote
cite="mid:CACy6zzJZszMvCiP-H+03jnij414omp3wk3Rq5Ahx_xcX+BJMSQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Simon and Cyril,
<div><br>
</div>
<div>I really appreciate your insight.</div>
<div><br>
</div>
<div>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
style="font-size:12.8px">SophiaBeads_512_averaged.</span></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">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></div>
<div><span style="font-size:12.8px"><br>
</span></div>
<div><span style="font-size:12.8px">Regards,</span></div>
<div><span style="font-size:12.8px">mg</span></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2016-01-20 3:33 GMT-05:00 Simon Rit <span
dir="ltr"><<a moz-do-not-send="true"
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 dir="ltr">
<div>
<div>
<div>
<div>Hi,<br>
</div>
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.<br>
</div>
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.<br>
</div>
Good luck,<br>
</div>
Simon<br>
</div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jan 19, 2016 at 8:02
PM, MG Vallet <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:mgvallet.pro@gmail.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:mgvallet.pro@gmail.com">mgvallet.pro@gmail.com</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Thanks Cyril!
<div>going to carefully check my inputs and I
give you some news.</div>
<div>mgv</div>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2016-01-19 10:33
GMT-05:00 Cyril Mory <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:cyril.mory@uclouvain.be"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:cyril.mory@uclouvain.be">cyril.mory@uclouvain.be</a></a>></span>:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
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
<div>
<div><br>
<br>
<div>Le 19/01/2016 16:19, MG
Vallet a écrit :<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">Dear rtk-users,
<div><br>
</div>
<div>I applied the <font
color="#000000"
face="Courier New"><span
style="font-size:12px">FDKConeBeamReconstructionFilter
to a data set from </span></font><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;font-size:14px;line-height:20px"><a
moz-do-not-send="true"
href="https://zenodo.org/record/16539"
target="_blank"><a class="moz-txt-link-freetext" href="https://zenodo.org/record/16539">https://zenodo.org/record/16539</a></a>. </span></div>
<div><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">This
is a plastic tube filled
with glass beads that has
been scanned.</span></div>
<div><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px"><br>
</span></div>
<div><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">Attached
is a view of the
reconstructed central
slice. It is found that:</span></div>
<div>
<ol>
<li><font color="#333333"
face="Roboto,
sans-serif"><span
style="line-height:20px">the
beads are quickly
deformed outside the
center</span></font></li>
<li><font color="#333333"
face="Roboto,
sans-serif"><span
style="line-height:20px">each
one has a halo, or a
shadow (dont know
the proper term)</span></font></li>
</ol>
</div>
<div><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">My
question is if these are
simply expected
artifacts. </span><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">I
am not 100% sure I
properly set the geometry
parameters.</span></div>
<div><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px"><br>
</span></div>
<div><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">Regards,</span></div>
<div><span
style="color:rgb(51,51,51);font-family:Roboto,sans-serif;line-height:20px">mgv</span></div>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
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