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Hi Simon and Andy,<br>
<br>
The ScaleFactor we use at VCU is a rough conversion from linear
attenuation coefficient (the output of RTK) to something roughly
around CT number (Hounsfield Units). This is not a proper
conversion, just a placeholder for now. I'm not sure how useful the
HNC-compatible version we have at VCU will be to the wider
community, as HNC is not a generally available format and HND is the
more common one. Are there any other users of RTK that use Varian
HNC format projections?<br>
<br>
Geoff <br>
<br>
<div class="moz-cite-prefix">On 11/23/12 6:35 AM, Andy Shieh wrote:<br>
</div>
<blockquote
cite="mid:CALqm++KH+v_enws+iLovmwPLOdd313=G2Y+04D4n380AmdHRyg@mail.gmail.com"
type="cite">Hi Simon,
<div><br>
</div>
<div>Just to let you know that the code works well!! Thanks!</div>
<div><br>
</div>
<div>By the way, I've been contacting with A/Prof Geoff Hugo (I
believe you know him?), and he mentioned that he's been putting
quite some effort on making RTK compatible with Varian format
(HNC mainly). He mentioned that for the Varian format, we
usually read in the "Norm Chamber value" (It's usually around
300) from each HNC header, and calculate the CT number by
log(NormChamberValue/Intensity) * ScaleFactor, where the
ScaleFactor is around 10000. I'm not too sure about the details,
but I believe he will discuss it with you soon when he has time!</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Andy<br>
<div class="gmail_extra"><br>
<div class="gmail_quote">
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<div class="h5">
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<div class="gmail_extra">
<br>
<br>
<div class="gmail_quote">2012/11/19 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">
Hi Andy,<br>
I have pushed a fix for the Varian raw to
attenuation conversion. Let<br>
me know if it meets what you've done. I will
let you know if there is<br>
any other improvement of the conversion in the
future.<br>
<span><font color="#888888">Simon<br>
</font></span>
<div>
<div><br>
On Fri, Nov 9, 2012 at 9:03 AM, Simon Rit<br>
<<a moz-do-not-send="true"
href="mailto:simon.rit@creatis.insa-lyon.fr"
target="_blank">simon.rit@creatis.insa-lyon.fr</a>>
wrote:<br>
> Hi Andy,<br>
><br>
> On Thu, Nov 8, 2012 at 5:58 PM, Andy
Shieh <<a moz-do-not-send="true"
href="mailto:hsieandy@gmail.com"
target="_blank">hsieandy@gmail.com</a>>
wrote:<br>
>> Hi Simon,<br>
>><br>
>> Thank you. At the moment I'm just
doing something similar to what you did<br>
>> for the Elekta system - using a
log_ref (I'm using HND_INTENSITY_MAX) and<br>
>> minus the log of intensity plus
one (I assume the plus one is to avoid<br>
>> taking the log of zero?).<br>
> Does it improve the results? You are
welcome to share it if you feel<br>
> that this is of interest for other
people.<br>
><br>
>><br>
>> Another few question:<br>
>> 1. Are you doing any
normalization after reconstruction or
forward<br>
>> projection?<br>
> No. Assuming you have line integral
of the attenuation as input of the<br>
> reconstruction algorithm, you get the
attenuation.<br>
><br>
> Are the negative values in the
reconstructed images simply a<br>
>> result of the ramp filtering?<br>
> Probably. You can use rtkprojections
to look at what is the input of<br>
> the reconstruction algorithm.<br>
><br>
>> 2. If I want to compare a
reprojection from an image reconstructed
using RTK<br>
>> with the original projection, how
should I make sure the normalization is<br>
>> correct? i.e. should I plus/minus
or multiply the reprojected attenuation<br>
>> before I use exponential and make
it back to intensity values?<br>
> You basically have to do the inverse
formula to what you have done. An<br>
> easy way of looking at what is going
on with forward projections is to<br>
> look at this example:<br>
> <a moz-do-not-send="true"
href="http://wiki.openrtk.org/index.php/RTK/Scripts/ForwardProjection"
target="_blank">http://wiki.openrtk.org/index.php/RTK/Scripts/ForwardProjection</a><br>
><br>
>> 3. The rtkforward projections
doesn't seem to work correctly when I'm<br>
>> projecting using a geometry file
containing several Projection (Angle). The<br>
>> output mha file seems to "repeat"
after a couple of projections instead of<br>
>> showing all projections. I'm
testing this on a Varian Half Fan geometry
- it<br>
>> works fine if I break the
geometry file down into one each for each<br>
>> projection angle and do the
forward projection separately. I can send
you a<br>
>> reprojection mha file if my
description is unclear to you.<br>
> I works for me. Would you be able to
fill in a bug report<br>
> (<a moz-do-not-send="true"
href="http://bug.openrtk.org/"
target="_blank">http://bug.openrtk.org/</a>)
with an example? You can generate volumes<br>
> and projections with
rtkdrawgeometricphantom and<br>
> rtkprojectgeometricphantom.<br>
> Simon<br>
><br>
>><br>
>> Thanks Simon!!<br>
>><br>
>> Cheers,<br>
>> Andy.<br>
>><br>
>><br>
>><br>
>> 2012/10/24 Simon Rit <<a
moz-do-not-send="true"
href="mailto:simon.rit@creatis.insa-lyon.fr"
target="_blank">simon.rit@creatis.insa-lyon.fr</a>><br>
>>><br>
>>> Hi Andy,<br>
>>> Yes you're right, I have
actually noticed recently that but I have
not<br>
>>> worked a lot on Varian images
because we don't have a Varian CBCT in<br>
>>> Lyon. I only had a
sub-sampled acquisition from Greg of a
Catphan that<br>
>>> I used to roughly check the
geometry. As far as I can remember, when I<br>
>>> wrote this piece of code, I
tried to use the same code as Plastimatch<br>
>>> but I could well have done it
wrongly. I'm actually waiting for a new<br>
>>> complete Catphan acquisition
from Greg to correct for this but if you<br>
>>> already have a patch to
suggest or a set of images to send, feel
free<br>
>>> to do it.<br>
>>> Thanks,<br>
>>> Simon<br>
>>><br>
>>> On Tue, Oct 23, 2012 at 2:48
PM, Andy Shieh <<a
moz-do-not-send="true"
href="mailto:hsieandy@gmail.com"
target="_blank">hsieandy@gmail.com</a>>
wrote:<br>
>>> > Hi Simon,<br>
>>> ><br>
>>> > I was looking at
"rtkVarianObiRawImageFilter.h", and
realized that the<br>
>>> > attenuation is
calculated from the projection image
simply via a<br>
>>> > negative<br>
>>> > transformation
(1-Intensity/HND_MaxIntensity).<br>
>>> > Is it usually the way
this is done, and is there any reason for
doing<br>
>>> > this?<br>
>>> > I would have thought
attenuation should be calculated from
intensity via<br>
>>> > logarithm (since I=I_0
exp(-mu x)).<br>
>>> > Thanks!!<br>
>>> ><br>
>>> > Cheers,<br>
>>> > Andy<br>
>>> ><br>
>>> >
_______________________________________________<br>
>>> > Rtk-users mailing list<br>
>>> > <a
moz-do-not-send="true"
href="mailto:Rtk-users@openrtk.org"
target="_blank">Rtk-users@openrtk.org</a><br>
>>> > <a
moz-do-not-send="true"
href="http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users"
target="_blank">http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users</a><br>
>>> ><br>
>><br>
>><br>
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<pre class="moz-signature" cols="72">--
------------------------------------
Geoffrey D. Hugo, Ph.D.
Assistant Professor
Dept. of Radiation Oncology
Virginia Commonwealth University
<a class="moz-txt-link-abbreviated" href="mailto:gdhugo@vcu.edu">gdhugo@vcu.edu</a></pre>
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