[Rtk-users] bright circle on the reconstructed image

[Howard]

Hi Cyril,

I am testing SART reconstruction according to what you described,
specifying dimension, spacing and origin:

rtksart \
   --geometry varianGeometry \
   --regexp .*.hnd \
   --path ../Scan0 \
   --output sart_rec.mha \
   --verbose \
   --spacing 2.0\
   --dimension 128,100,128 \
   --origin -127.5,-99,-127.5

but the reconstruction gave a plain image with no object/contrast. I
checked the grayscale values on the reconstructed images and did see they
ranged from -1.78 to 3 (this may not be precise but give you some idea). I
tried to adjust window level but couldn't see any contrast. I must miss
something here. Please advise. Thanks!

-howard

On Thu, Sep 18, 2014 at 10:59 AM, Cyril Mory <
cyril.mory at creatis.insa-lyon.fr> wrote:

>  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
> > 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> 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
>>>
>>>
>>>   _______________________________________________
>>> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>> --
>>> --
>>> 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
>>>
>>>
>>> _______________________________________________
>>> Rtk-users mailing list
>>> Rtk-users at public.kitware.com
>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>
>>>
>>
>
> --
> --
> 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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/rtk-users/attachments/20140918/bbd05a47/attachment-0009.html>