[Rtk-users] bright circle on the reconstructed image

[Simon Rit]

Hi Howard,
Assuming you're using the same dataset as the one you used for the
rtkfdk test, you have decreased its size. For example, x was 2*256 mm
with rtkfdk and it is now 128*2. On the slice you sent, we could see
that a part of the phantom on the right was missing so you should keep
the same size except for this side that should be larger, certainly
not reduce the size.
For the display, I would suggest to use the same window/level as for
your FDK reconstruction. The two reconstruction algorithms reconstruct
the same average intensities, only the texture is different.
Good luck,
Simon

On Thu, Sep 18, 2014 at 7:03 PM, Howard <lomahu at gmail.com> wrote:
> 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 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
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>
>