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<div class="moz-cite-prefix">On 02/09/2016 11:53, Lukas Gromann
wrote:<br>
</div>
<blockquote cite="mid:99EB4A21-68E1-4CE8-96C0-C97723A8D452@tum.de"
type="cite">
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Hi Simon,
<div><br>
</div>
<div>thanks for your fast reply, this helps me already a lot.
Indeed I read those parts in the wiki and had also a short
look at the papers mentioned. </div>
<div><br>
</div>
<div>Especially the following questions still arise for me: </div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>-
What are the „signals“ in primary, total, compton etc? Are
these detection probabilities? Photon counts? Or total
recorded Photon-Energies per pixel, or is this converted to
some arbitrary ADU-values?</div>
</blockquote>
There is a detector response curve that will set this. This is a
text file in which the first column is the incoming photon energy
(in MeV) and the second column is the detected signal. It's used
both in the Monte Carlo and the fixed forced detection examples, I
first describe it for Monte Carlo where you have one photon
arriving on the pixel at a time. If you don't set it, it will
integrate the energy of the incoming photons, which would be
similar to setting it to a ramp:<br>
0 0<br>
1 1<br>
Note that the values are linearly interpolated.<br>
<br>
The other option is to do a photon counting, so to add 1
regardless of the energy:<br>
0 1<br>
1 1<br>
<br>
You can also set a much more complex (but more realistic)
function, as described in <a moz-do-not-send="true"
href="dx.doi.org/10.1088/0031-9155/53/22/003">[Roberts et al,
PMB, 2008]</a> which we recently used in <a
moz-do-not-send="true"
href="http://dx.doi.org/10.1118/1.4961400">[Vilches-Freixas et
al, Med Phys, 2016]</a>. I have enclosed an example.<br>
<br>
Now, for fixed forced detection, the final value is also
multiplied by the probability of having a photon with that energy
in this pixel since this is what FFD computes.<br>
<br>
<blockquote cite="mid:99EB4A21-68E1-4CE8-96C0-C97723A8D452@tum.de"
type="cite">
<div><span class="Apple-tab-span" style="white-space:pre"></span>- I
guess this is related to the energy-response of the detector?
Also here the example provides some
basic responseDetector.txt, but the Syntax is not clear to me.</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>-
In the example Code, there is an option called
„/gate/actor/ffda/energyResolvedBinSize 0 keV“, which
is not mentioned in the wiki at all. If I would set this Value
to 1keV, would I create a Photon counting detector with 120
energy bins? How would the Output look like? 120 images each
for „compton“ and <span class="Apple-tab-span" style="white-space:pre"></span>"primary“?
<br>
</div>
</blockquote>
Yes, these are recent (unreleased) dev. If you set this to a non 0
value, instead of storing 2D projection images, it stores 3D
projection images where the third dimension is the energy. There
is still one projection only per gantry angle. Indeed, if your max
spectrum energy, it would create 120 energy bins with a perfect
energy resolved detector.<br>
<blockquote cite="mid:99EB4A21-68E1-4CE8-96C0-C97723A8D452@tum.de"
type="cite">
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>I would therefore suggest to add at least the following
lines to the documentation: </div>
<div>
<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000">
<p>All contributions are summed in total which can be
decomposed in primary+secondary. Secondary (same as
scatter) can itself be decomposed in
compton+rayleigh+fluorescence. flatfield is available to
compute the measured primary signal if there is no
object, this is useful for CT to apply the beer Lambert
law. attenuation is ln(flatfield/primary) to get the
line integral, i.e., the input of most CT reconstruction
algorithms.</p>
</div>
</blockquote>
</div>
<div><br>
</div>
</blockquote>
Yep, will do + what I just say. I suggest to continue the
discussion when something is not clear and I'll summarize soon on
the wiki. Keep asking!<br>
<blockquote cite="mid:99EB4A21-68E1-4CE8-96C0-C97723A8D452@tum.de"
type="cite">
<div> </div>
<div><br>
</div>
<div>Thanks, </div>
<div><br>
</div>
<div>Lukas </div>
<div><br>
<div>
<div apple-content-edited="true">
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orphans: auto; text-align: start; text-indent: 0px;
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-webkit-line-break: after-white-space;">
<div>----------------------------------------------------</div>
<div>Lukas Gromann</div>
<div><br>
</div>
<div>Lehrstuhl für Biomedizinische Physik (E17)<br>
Technische Universität München<br>
Boltzmannstrasse 11<br>
85748 Garching<br>
<br>
</div>
<div><a moz-do-not-send="true"
href="mailto:Lukas.Gromann@TUM.de">Lukas.Gromann@TUM.de</a></div>
<div><br>
</div>
<div>Tel.: 089-289/10905</div>
<div>Mobil: 017629718306</div>
</div>
</div>
<br>
<div>
<div>Am 02.09.2016 um 11:02 schrieb Simon Rit <<a
moz-do-not-send="true"
href="mailto:simon.rit@creatis.insa-lyon.fr">simon.rit@creatis.insa-lyon.fr</a>>:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#FFFFFF" text="#000000">
<p>Hi,</p>
<p>I assume you've read</p>
<p><a moz-do-not-send="true"
href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.2:Readout_parameters_for_Radiotherapy_applications:_Actors#Fixed_Forced_Detection_CT">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.2:Readout_parameters_for_Radiotherapy_applications:_Actors#Fixed_Forced_Detection_CT</a>?</p>
<p>It's scarce but there are a bunch of references we
suggest to understand the technique. The numbers are
the expected signal in the image. All contributions
are summed in total which can be decomposed in
primary+secondary. Secondary (same as scatter) can
itself be decomposed in
compton+rayleigh+fluorescence. flatfield is
available to compute the measured primary signal if
there is no object, this is useful for CT to apply
the beer Lambert law. attenuation is
ln(flatfield/primary) to get the line integral,
i.e., the input of most CT reconstruction
algorithms.</p>
<p>An alternative is to do pure monte carlo, see
monteCarloCT.mac in the same folder. I guess there
are other options in Gate but I don't know all the
CT options in Gate. Please let me know if you find
some!</p>
<p>Hope this helps and let us know if/how we should
complete the "doc",</p>
<p>Simon<br>
</p>
<br>
<div class="moz-cite-prefix">On 02/09/2016 09:49,
Lukas Gromann wrote:<br>
</div>
<blockquote
cite="mid:2F51EFFD-7854-4884-938E-85F6C34E9676@tum.de"
type="cite">Dear all,
<div><br>
</div>
<div>I am currently learning how to use Gate for my
PHD project in medical x-rax imaging.</div>
<div><br>
</div>
<div>I would like to simulate the Compton scatter
fraction in a simple Thorax x-ray. I started by
using the example_CT/fixedForcedDetectionCT, which
looks like the thing I am looking for.
Unfortunately I cannot find any documentation,
what is actually the content of the outputfiles
created by the FixedForcedDetection actor. What
does the numbers in the various images represent?
What is the purpose of the flatfield file?</div>
<div>Any kind of additional
documentation/information would be very welcome! </div>
<div><br>
</div>
<div>On the other hand, is there maybe a much better
approach to determine Compton scatter fractions in
my images than using the FFD actor? </div>
<div><br>
</div>
<div>Thanks for your help, </div>
<div><br>
</div>
<div>Lukas </div>
<div><br>
</div>
<div apple-content-edited="true">
<div style="letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;">
<div>----------------------------------------------------</div>
<div>Lukas Gromann</div>
<div><br>
</div>
<div>Lehrstuhl für Biomedizinische Physik (E17)<br>
Technische Universität München<br>
Boltzmannstrasse 11<br>
85748 Garching<br>
<br>
</div>
<div><a moz-do-not-send="true"
href="mailto:Lukas.Gromann@TUM.de">Lukas.Gromann@TUM.de</a></div>
<div><br>
</div>
<div>Tel.: 089-289/10905</div>
<div>Mobil: 017629718306</div>
</div>
</div>
<br>
<br>
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<br>
<div class="moz-cite-prefix">On 02/09/2016 09:49,
Lukas Gromann wrote:<br>
</div>
<blockquote
cite="mid:2F51EFFD-7854-4884-938E-85F6C34E9676@tum.de"
type="cite">Dear all,
<div><br>
</div>
<div>I am currently learning how to use Gate for my
PHD project in medical x-rax imaging.</div>
<div><br>
</div>
<div>I would like to simulate the Compton scatter
fraction in a simple Thorax x-ray. I started by
using the example_CT/fixedForcedDetectionCT, which
looks like the thing I am looking for.
Unfortunately I cannot find any documentation,
what is actually the content of the outputfiles
created by the FixedForcedDetection actor. What
does the numbers in the various images represent?
What is the purpose of the flatfield file?</div>
<div>Any kind of additional
documentation/information would be very welcome! </div>
<div><br>
</div>
<div>On the other hand, is there maybe a much better
approach to determine Compton scatter fractions in
my images than using the FFD actor? </div>
<div><br>
</div>
<div>Thanks for your help, </div>
<div><br>
</div>
<div>Lukas </div>
<div><br>
</div>
<div apple-content-edited="true">
<div style="letter-spacing: normal; orphans: auto;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;">
<div>----------------------------------------------------</div>
<div>Lukas Gromann</div>
<div><br>
</div>
<div>Lehrstuhl für Biomedizinische Physik (E17)<br>
Technische Universität München<br>
Boltzmannstrasse 11<br>
85748 Garching<br>
<br>
</div>
<div><a moz-do-not-send="true"
href="mailto:Lukas.Gromann@TUM.de">Lukas.Gromann@TUM.de</a></div>
<div><br>
</div>
<div>Tel.: 089-289/10905</div>
<div>Mobil: 017629718306</div>
</div>
</div>
<br>
<br>
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