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Hi Guangming,<br>
<br>
I have just tested your command line and obtained some result,
although it is indeed disappointing. SART generates strong artifacts
on the borders of the image because some rays intersect only a few
voxels on the borders and make the convergence very unstable. These
artifacts are intense, so they mess up with the automatic choice of
the window and level of the viewer.<br>
<br>
My advice : <br>
- Use "VV, the 4D slicer" to open your data (you should not see much
at the beginning), and in the top right viewing pane, click in the
center and hit the 'w' key. It will look at the pixels around the
one you clicked, and adjust the window / level accordingly. Then you
should see the reconstruction and the artifacts at the borders. Any
other viewer with this "local windowing" option should do fine.<br>
- If you want to reconstruct a full volume, not just one slice, you
can use SART : the artefacts on the borders should be much less
intense once your whole object is in the reconstructed volume<br>
- If you want to reconstruct a single slice, or a few slices, use
"rtkconjugategradient" instead. It does essentially the same as
SART, but has a way steadier (although a bit slower) convergence.
You can run it with the same options as SART, so all you have to do
is replace "rtksart" by "rtkconjugategradient" in your command line
examples (in particular, it runs fine on CUDA)<br>
<br>
Do not hesitate to ask if you happen to have more questions.<br>
Regards,<br>
<br>
Cyril<br>
<br>
<div class="moz-cite-prefix">On 11/20/2014 01:08 PM, Guangming Zang
wrote:<br>
</div>
<blockquote
cite="mid:CAD0jwngMBpJ29th8-3iKJOeU1tEe9_DsOzstzvGBVtJGOA6vMw@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>BTW, the Varian reconstruction has the same situation.I
tested just now that fdk work well while sart not.</div>
<div><br>
</div>
<div>Best </div>
<div>Guangming</div>
<div>
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<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Guangming Zang</b> <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:guangming.zang@kaust.edu.sa">guangming.zang@kaust.edu.sa</a>></span><br>
Date: 2014-11-20 14:21 GMT+03:00<br>
Subject: some bugs in SART when running Reconstruction of
Elekta Data<br>
To: "<a moz-do-not-send="true"
href="mailto:rtk-users@public.kitware.com">rtk-users@public.kitware.com</a>"
<<a moz-do-not-send="true"
href="mailto:rtk-users@public.kitware.com">rtk-users@public.kitware.com</a>><br>
<br>
<br>
<div dir="ltr">Hi,
<div>i ran the Reconstruction of Elekta Data example in wiki</div>
<div> (<a moz-do-not-send="true"
href="http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction"
target="_blank">http://wiki.openrtk.org/index.php/RTK/Examples/ElektaReconstruction</a>)</div>
<div>when i use fdk to reconstruct the data, it work very
well(can see the slice). When ran the SART algorithm,
however,i got the result with same size of fdk algorithm's
, but nothing can been seen in the slice.</div>
<div>Here is the command i used:</div>
<div>fdk:</div>
<div> rtkfdk --geometry elektaGeometry --path
img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his
--output slice29.5.mha --spacing 0.25,0.25,0.25
--dimension 1024,1,1024 --origin -127.875,29.5,-127.875<br>
</div>
<div><br>
</div>
<div>SART(with different -f -b):</div>
<div> rtksart --geometry elektaGeometry --path
img_1.3.46.423632.135428.1351013645.166/ --regexp .*.his
--output slice29.6.mha --spacing 0.25,0.25,0.25
--dimension 1024,1,1024 --origin -127.875,29.5,-127.875<br>
</div>
<div><br>
</div>
<div>
<div>rtksart -g elektaGeometry -f CudaRayCast -b
CudaVoxelBased -t 1 -p
img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o
slice_cuda.mha --spacing 0.25,0.25,0.25 --dimension
1024,1,1024 --origin -127.875,29.5,-127.875</div>
</div>
<div><br>
</div>
<div>
<div>rtksart -g elektaGeometry -f Joseph -b
NormalizedJoseph -t 1 -p
img_1.3.46.423632.135428.1351013645.166/ -r .*.his -o
slice.mha --spacing 0.25,0.25,0.25 --dimension
1024,1,1024 --origin -127.875,29.5,-127.875</div>
</div>
<div>the results are the same, can not see anything.</div>
<div><br>
</div>
<div>Can you help me to figure it out or give me some
suggestions?</div>
<div>Thanks for your time.</div>
<div>
<div>
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<pre class="moz-signature" cols="72">--
--
Cyril Mory, Post-doc
CREATIS
Leon Berard cancer treatment center
28 rue Laënnec
69373 Lyon cedex 08 FRANCE
Mobile: +33 6 69 46 73 79</pre>
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