[Rtk-users] bright circle on the reconstructed image

[Cyril Mory]

Howard,

For SART reconstructions, you do not need padding, and you can't do Hann 
windowing because no ramp filtering is applied. SART usually outputs 
smoother images, so you probably will not need this denoising trick anyway.
However, you should be careful about one thing : your object has to be 
fully contained in the reconstructed volume, or you will observe 
important border effects. Use the --dimension, --spacing and --origin 
options to ensure this.

All the best,
Cyril

On 09/18/2014 04:47 PM, Howard wrote:
> Thanks very much, Cyril & Simon. Now the fdk reconstruction is working 
> beautifully. Jus another quick question: for rtksart executable, are 
> we still able to do padding and hanning window trick as well?
>
> On Thu, Sep 18, 2014 at 9:47 AM, Simon Rit 
> <simon.rit at creatis.insa-lyon.fr 
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
>     Hi,
>     I fully agree with Cyril. Something else : you might want to mask
>     out what is outside the field-of-view using the rtkfieldofview
>     executable. Your ring corresponds to that border. See an example here:
>     http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction
>     Simon
>
>     On Thu, Sep 18, 2014 at 10:12 AM, Cyril Mory
>     <cyril.mory at creatis.insa-lyon.fr
>     <mailto:cyril.mory at creatis.insa-lyon.fr>> wrote:
>
>         Hi Howard,
>
>         The bright ring artifact is typically caused by high-pass
>         filtering (the ramp filter used in FDK) of truncated
>         projection data (when projections have non-zero values on the
>         sides, the edge of the projection makes a sharp transition to
>         zero). A classical answer to this problem is to pad the
>         projections, for example with values starting from the values
>         on the side and slowly decreasing to zero.
>
>         rtkfdk can do this padding for you. Just add "--pad 0.1" to
>         your options (or more than 0.1 if it isn't enough).
>         Also, I noticed that your reconstructed image seems quite
>         noisy. You might want to use a Hann windowing of the ramp
>         filter to reduce the noise amplification effect of high-pass
>         filtering. You can do that by adding "--hann 0.5" to your
>         options. Note that the argument is a cut-off frequency, so
>         smaller values mean more smoothing.
>
>         Best regards,
>         Cyril
>
>
>         On 09/18/2014 05:21 AM, Howard wrote:
>>         Hi,
>>         I use rtkfdk to reconstruct varian cbct images following the
>>         example on rtk wiki page. The projections were obtained with
>>         half fan mode because it is an abdominal region with the
>>         patient lateral x AP dimension of 550x550. The reconstructed
>>         cbct images have a big bright circle around
>>         the image. Please see the image:
>>         http://expirebox.com/download/2f55c9d8f0bc83138b954d2fec08e78c.html
>>         I am using Ubuntu Linux box to reconstruct. Two sequential
>>         commands were used:
>>         ./rtkvarianobigeometry --xml_file ProjectionInfo.xml --path
>>         Scan0/ --regexp Proj_.*.hnd -o varianGeometry
>>         and
>>         rtkfdk \
>>            --geometry varianGeometry \
>>            --regexp .*.hnd \
>>            --path ../Scan0 \
>>            --output rec.mha \
>>            --verbose \
>>            --spacing 2.0,2.0,2.0 \
>>            --dimension 256,100,256 \
>>         The projections are stored in the standard varian format:
>>         Scan0 and ProjectionInfo.xml with 644 projection images.  I
>>         assume that rtkfdk handled the half fan geometry properly.
>>         What did I do wrong then?  Many thanks!
>>         -howard
>>
>>
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>
>         -- 
>         --
>         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  <tel:%2B33%206%2069%2046%2073%2079>
>
>
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>
>

-- 
--
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

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