<div dir="ltr">Hi Simon,<div><br></div><div>I also got a question about how the weighting is performed.</div><div><br></div><div>Before the question, first of all there may be an error in rtk::ThreeDCircularProjectionGeometry::GetAngularGapsWithNext(...). I cannot see the reason for the factor 0.5 in the following code:</div><div><div> //Last projection wraps the angle of the first one</div><div> angularGaps[curr->second] = 0.5 * ( sangles.begin()->first + 2*vnl_math::pi - curr->first );</div></div><div>If this is indeed wrong, then the max gap can be underestimated in the ParkerShortScanImageFilter, which you use for the 20 degree condition.</div><div><br></div><div>Then here's the question: why does RTK eliminate the first and last projections before calculating the weights? The Parker weights are already all zeros for the first and the last projections involved in the calculation. If you rule out the first and the last projection in the data set in advance, you then have four projections with zeros and the effective scan angle is smaller then the actual short scan, which may lead to an insufficient data problem.</div><div><br></div><div>Best regards,</div><div>Chao</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2015-12-18 18:18 GMT+01:00 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 Shiras,<br>
Sorry for the delayed answer, times are busy. The way RTK computes
the spanned arc is from the second projection angle to the before
last projection angle, i.e., in your case<br>
209.609216488925-11.6067737022482<br>
so it's a span of 199 degrees and your cone angle is indeed too
large. Like I said, this part of RTK is perfectible and there is no
way to change this but change the code.<br>
However, the source of artefacts might be something else. On
simulated data, I tried:<br>
rtkprojectshepploganphantom --like original_proj.mhd -g
geometry_parker_corr.xml -o proj.mha<br>
rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml<br>
and the result is not that bad. What do you think? Can you show us a
snapshot if sg's wrong in your opinion?<span class="HOEnZb"><font color="#888888"><br>
Simon</font></span><div><div class="h5"><br>
<br>
<div>On 09/12/2015 11:01, Shiras Abdurahman
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Dear Simon,
<div><br>
</div>
<div>I am attaching the mhd files of projections.</div>
<div><br>
</div>
<div>With regards,</div>
<div>Shiras</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Dec 8, 2015 at 6:17 PM, Simon
Rit <span dir="ltr"><<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</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">
<div>
<div>Hi,<br>
</div>
The geometry files look ok to me. What is the projection
information? If you're still getting the same message as
before, I think it's because you don't have enough data.
If you send the mhd file of the projections (just the
mhd, not the raw data), I can try to test it on
simulated data to let you know my feeling.<span><font color="#888888"><br>
</font></span></div>
<span><font color="#888888">Simon<br>
</font></span></div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Dec 8, 2015 at 5:41
PM, Shiras Abdurahman <span dir="ltr"><<a href="mailto:shiraska@gmail.com" target="_blank"></a><a href="mailto:shiraska@gmail.com" target="_blank">shiraska@gmail.com</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">Dear Simon,
<div><br>
</div>
<div>I tried this option and unfortunately it
did not work. I added zero projections and
modified geometry files. However, I am getting
same artifacts in the volume. Voxel values
changed a little bit that indicates during
backprojection it still considers extreme
projections. I am also getting an output
message same as before.</div>
<div><br>
</div>
<div>I am attaching geometry files.</div>
<div><br>
</div>
<div>With regards,</div>
<div>Shiras</div>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Dec 8, 2015
at 10:15 AM, Simon Rit <span dir="ltr"><<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>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>So calling AddProjection before
and after the loop with an adequate
gantry_angle should work.<span><font color="#888888"><br>
</font></span></div>
<span><font color="#888888">Simon<br>
</font></span></div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue,
Dec 8, 2015 at 9:52 AM, Shiras
Abdurahman <span dir="ltr"><<a href="mailto:shiraska@gmail.com" target="_blank"></a><a href="mailto:shiraska@gmail.com" target="_blank">shiraska@gmail.com</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">Drear Simon,
<div><br>
</div>
<div>I generate the geometry
with system geometry
parameters and using
AddProjection method.</div>
<div><br>
</div>
<div>Here is the code</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div><span style="white-space:pre-wrap"> </span>rtk::ThreeDCircularProjectionGeometry::Pointer
rtk_sys_geometry_;</div>
<div><span style="white-space:pre-wrap"> </span>rtk_sys_geometry_
=
rtk::ThreeDCircularProjectionGeometry::New();</div>
<div><span style="white-space:pre-wrap"> </span>for
(uint16_t proj_index =
0; proj_index <
num_projections_;
proj_index++)</div>
<div><span style="white-space:pre-wrap"> </span>{</div>
<div><span style="white-space:pre-wrap"> </span>rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm,</div>
<div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).sdd_mm,</div>
<div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).gantry_angle_deg,</div>
<div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).proj_offset_x_mm,</div>
<div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).proj_offset_y_mm,</div>
<div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).out_plane_angle_deg,</div>
<div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).in_plane_angle_deg,</div>
<div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).src_offset_x_mm,</div>
<div><span style="white-space:pre-wrap"> </span>rtk_geom_params_.at(proj_index).src_offset_y_mm);</div>
<div><span style="white-space:pre-wrap"> </span>}</div>
</div>
<div><br>
</div>
<div><span style="white-space:pre-wrap"> And then write to xml file.</span></div>
<span><font color="#888888">
<div><br>
</div>
<div>Shiras</div>
<div><br>
</div>
<div><br>
</div>
</font></span></div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
Tue, Dec 8, 2015 at
9:23 AM, Simon Rit <span dir="ltr"><<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>
wrote:<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>
<div>
<div>Hi,<br>
</div>
rtkfdk.cxx
just read the
geometry from
a file so the
best is to
modify the
geometry file.
How do you
generate the
geometry?<br>
</div>
For example,
if you use
rtksimulated
geometry,
let's say that
you were
using:<br>
</div>
rtksimulatedgeometry
-n 200 -a 200
-o g.xml<br>
</div>
then you'll
have to
replace it
with<br>
rtksimulatedgeometry
-n 202 -a 202
-o g.xml -f -1<br>
</div>
Don't forget to
add dummy
projection at
the beginning
and the end. If
you use a more
complex
geometry, maybe
<a href="http://wiki.openrtk.org/index.php?title=SimpleRTK" target="_blank">SimpleRTK</a>
can be helpful
(I'd use that)
or you'd have to
modify the cxx
code to add
these additional
projections in
the geometry and
the projection
stack.<span><font color="#888888"><br>
</font></span></div>
<span><font color="#888888">Simon<br>
<div>
<div>
<div><br>
</div>
</div>
</div>
</font></span></div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
Tue, Dec 8,
2015 at 8:51
AM, Shiras
Abdurahman <span dir="ltr"><<a href="mailto:shiraska@gmail.com" target="_blank"></a><a href="mailto:shiraska@gmail.com" target="_blank">shiraska@gmail.com</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">Dear
Simon,
<div><br>
</div>
<div>Thanks a
lot for the
reply. Can you
please inform
me how can I
set where the
arc starts?</div>
<div>Do I need
to modify
geometry also?</div>
<div>If you
can point the
line of code
rtkfdk.cxx, it
will be really
helpful.</div>
<div><br>
</div>
<div>With
regards,</div>
<div>Shiras</div>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On
Tue, Dec 8,
2015 at 7:56
AM, Simon Rit
<span dir="ltr"><<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>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><span>
Dear Shiras,<br>
Yes, for
practical
reasons the
first and the
last
projections
are set to 0
and the arc
used in the
Parker
weighting
starts between
the first two
projections
and ends
between the
lasts two
projections.
There is a
simple
solution: add
a projection
at the
beginning and
the end of the
arc, which can
contain any
pixel values
but should be
set where you
want this arc
to start. In
the future, I
think someone
should once
take the time
to correct
this but I
haven't so
far. I'll keep
you posted on
the mailing
list when it's
corrected.<br>
Simon<br>
<br>
<div>On
07/12/2015
12:04, Shiras
Abdurahman
wrote:<br>
</div>
</span>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">Hi
all,
<div><br>
</div>
<div>I am
trying to
reconstruct a
volume from
projection
data generated
with C-arm CT.
There are 248
projections
with an
angular range
of 199 degree.
Technically,
parker
weighting
should run
without any
problems.
However, I am
getting an
output message
that "You do
not have
enough data
for proper
parker
weighting".
After parker
weighting, the
two extreme
projections
(projection
number 1 and
248) were
completely
zero and thus
reconstructed
volume
contained
artifacts.
When I
increased the
angular range,
this problem
did not
happen. How
can I solve
this problem
without
increasing
angular range?
Is there any
threshold
constant that
I can change
in command
line or in my
code?</div>
<div><br>
</div>
<div>I really
appreciate any
help you can
provide.</div>
<div><br>
</div>
<div>With
regards,</div>
<div>Shiras</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
<span>
<pre>_______________________________________________
Rtk-users mailing list
<a href="mailto:Rtk-users@public.kitware.com" target="_blank">Rtk-users@public.kitware.com</a>
<a href="http://public.kitware.com/mailman/listinfo/rtk-users" target="_blank">http://public.kitware.com/mailman/listinfo/rtk-users</a>
</pre>
</span></blockquote>
<br>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
</div></div></div>
<br>_______________________________________________<br>
Rtk-users mailing list<br>
<a href="mailto:Rtk-users@public.kitware.com">Rtk-users@public.kitware.com</a><br>
<a href="http://public.kitware.com/mailman/listinfo/rtk-users" rel="noreferrer" target="_blank">http://public.kitware.com/mailman/listinfo/rtk-users</a><br>
<br></blockquote></div><br></div>