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<div class="moz-cite-prefix">Dear RTK-users,<br>
<br>
I am working on reconstruction with RTK backprojection algorithm.<br>
RTK Wiki examples worked fine but now, I am trying with my own
images, and I obtain a result I cannot explain.<br>
<br>
I have 15 projections, simulated with GATE. My phantom is a water
cylinder, containing 4 balls of different materials.<br>
I attached one of them with the mail, to give an example (the
other are quite similar, only the place of the balls changes).<br>
<br>
I generate a geometry.xml file with the command<b> </b>: <b>rtksimulatedgeometry
-o geometry.xml -n 15 --sdd 300 --sid 150</b><br>
and then apply rtkbackprojection with : <b>rtkbackprojections -o
output.mha -g geometry.xml </b><b>-r header.mhd -p.</b> <br>
I display output.mha with VTK and obtain a white cube...<br>
<br>
Does anybody have an idea of what I am missing? Is the number of
projections too small? Is it a display problem?<br>
<br>
Regards,<br>
<br>
Laura Trubuil<br>
<br>
<br>
<br>
Le 13/05/2013 16:14, Simon Rit a écrit :<br>
</div>
<blockquote
cite="mid:CAF0oig2j-r=V3z2fm_H06zaU8YUNvmyqRwS4iEptV3VzWPgLbQ@mail.gmail.com"
type="cite">
<pre wrap="">Dear Laura,
If you use rtk::FDKConeBeamReconstructionFilter, there is a weighting
by the angular gap (angular distance between the previous and the next
projection) so that will be a problem. If you only use the
backprojection, that should not be a problem.
With FDK, there are a few solutions, the simplest being to trick the
algorithm by adding 2 projections with zeros at the beginning and the
end of your tomosynthesis acquisition.
If you have some problems with the geometry, don't hesitate to provide
your Gate macros and we can try to help.
Simon
On Tue, May 7, 2013 at 10:05 AM, Laura Trubuil
<a class="moz-txt-link-rfc2396E" href="mailto:laura.trubuil@mail.medecom.fr"><laura.trubuil@mail.medecom.fr></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Simon,
Thank you for your help.
It is a circular cone beam CT, yes.
In fact, what I precisely do is working on tomosynthesis. I use the CT
scanner simulator of GATE as a basis for a tomosynthesis simulation. The
only differences are that the X-Ray dose is lower, and the angle is not 360°
but 40° maximum. I do not think it is a problem for RTK, is it?
First, I intend to use RTK backprojection, and then, I will try to enhance
the quality of the reconstruction by filtering techniques.
I have already done some simulations on GATE, for small animal in a first
time (because the computation time is too long for real human chest
detectors, which are much bigger). It allows me to work on algorithms and
test reconstruction with something, for the moment! I will be glad to help
you if I can.
I will continue studying RTK examples, I will let you know if I make some
progress. Thanks again.
Regards,
Laura
Le 07/05/2013 01:50, Simon Rit a écrit :
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
I don't know the CT simulation module of Gate so I can't help you. I
will discuss this matter with my colleagues. We are currently working
on a new CT simulation module but we definitely need to investigate
how one can reconstruct from the existing module. What is the geometry
of the scanner, is it circular cone-beam CT? It is the only geometry
that RTK can handle.
To understand how to use mhd files, you can look at other examples on
RTK wiki. We will work on your problem and I'll let you know as soon
as we have progressed but keep us informed if you make some progresses
on your side.
Regards,
Simon
On Mon, May 6, 2013 at 9:21 AM, Laura Trubuil
<a class="moz-txt-link-rfc2396E" href="mailto:laura.trubuil@mail.medecom.fr"><laura.trubuil@mail.medecom.fr></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Simon,
Thank you for your answer.
I am using the CT Scanner simulation in GATE, so the output available
are
the ".root" and the ".dat" only.
First, I simply tried to change the extension ".dat" to ".mhd" or to
".raw"
but, as expected, it does not work because I need to specifiy which kind
of
data the file contains (the role of the header in fact...).
Then, I tried to do something with the GateToImage Class, which contains
a
function called WriteMHD, but it was not a success... I did not find a
way
to directly obtain ".mhd" from a CT Scanner simulation from GATE. That is
when I decided to ask the RTK users!
With M. Mory's method, I am now able to open my ".dat" files with
ImageFileReader function from ITK, and visualize it with VTK.
For the moment, I am trying to reconstruct slices from 15 projections
acquired with the CT Scanner example in GATE.
Have you got any example of reconstruction of slices from projections
with
RTK?
I already studied the Sphere reconstruction tuto, but it does not help me
to
understand how I can make use of my ".mhd" files in the RTK algorithms. I
will do further research work.
Regards,
Laura Trubuil
Le 05/05/2013 11:20, Simon Rit a écrit :
</pre>
<blockquote type="cite">
<pre wrap="">Dear Laura,
I think that in the latest version of Gate, you should be able to
write mhd files. hdr file format should also work in both platforms.
What happens if you change the extension of your output files to .mhd?
Regards,
Simon
On Thu, May 2, 2013 at 10:51 AM, MORY, CYRIL <a class="moz-txt-link-rfc2396E" href="mailto:Cyril.Mory@philips.com"><Cyril.Mory@philips.com></a>
wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Laura,
In the .mhd and .raw format, the .raw file is a binary file of floats
(or
whatever) representing the pixel intensities, and the .mhd a simple
header
that indicates the number of dimensions, the size in pixels along each
dimension, ... Your .dat seems to be exactly the same as the .raw
You can create the .mhd header yourself, using a text editor. Here is
an
example :
ObjectType = Image
NDims = 2
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 1
Offset = -190.5 -190.5
CenterOfRotation = 0 0
ElementSpacing = 3 3
DimSize = 128 128
ElementType = MET_FLOAT
ElementDataFile = SheppLogan.raw (try to replace this field with your
.dat filename)
If I were you, I'd start by trying to adjust these parameters until you
manage to visualize a single projection (there are plenty of viewers
that
open mhd/raw files), and then create a header for the whole sequence
(NDims
= 3, etc ...) and concatenate the .dat binary files into a single one.
You
could use a script like the following :
#!/bin/bash
# Concatenate all projections into a single raw file
NbProj=300
i=0
list="projection${i}.raw"
for i in $(seq 1 1 $(($NbProj-1)))
do
list="$list projection${i}.raw"
done
cat $list > SheppLogan.raw
which would concatenate all files named "projection0.raw",
"projection1.raw", ... into "SheppLogan.raw"
-----Message d'origine-----
De : <a class="moz-txt-link-abbreviated" href="mailto:rtk-users-bounces@openrtk.org">rtk-users-bounces@openrtk.org</a>
[<a class="moz-txt-link-freetext" href="mailto:rtk-users-bounces@openrtk.org">mailto:rtk-users-bounces@openrtk.org</a>]
De la part de Laura Trubuil
Envoyé : jeudi 2 mai 2013 09:29
À : <a class="moz-txt-link-abbreviated" href="mailto:rtk-users@openrtk.org">rtk-users@openrtk.org</a>
Objet : [Rtk-users] .dat to .mha image
Dear RTK users,
I am working on GATE (from Geant4), to create projections images of
tomosynthesis.
I have projections but they are in ".dat" format (binary matrix of
float
numbers that stores the simulated tomosynthesis image and is produced
for
each time slice).
I want to reconstruct a 3D volume, from projections, with RTK.
To do that, I know I must change the format of my images (for example
to
.mhd/.raw or to .mha format) but my problem is that I do not know how.
I anyone could help...
Regards,
Laura
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