[Rtk-users] bright circle on the reconstructed image

Thu Sep 18 23:47:51 CEST 2014

Hi Simon,

I apologize for the confusion about the dataset. Actually I did not use the
same dataset.
The reason is that the set I used for rtkfdk test had 644 projections and
with it rtksart
crashed because of memory (I only allocated 3GB memory to Virtualbox from
my window7).
So for the SART test I changed to a small projection set (366 projections)
where the object is
a cube with dimension of 5cm x 5cm x 5cm. That's why I chose a smaller
reconstruction
size 128*2. With the same dataset when I ran rtkfdk I got very good
reconstruction.

-howard

On Thu, Sep 18, 2014 at 4:41 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> 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
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20140918/6c9117cb/attachment.htm>