[Rtk-users] Parker weighting
Simon Rit
simon.rit at creatis.insa-lyon.fr
Fri Dec 18 18:18:03 CET 2015
Hi Shiras,
Sorry for the delayed answer, times are busy. The way RTK computes the
spanned arc is from the second projection angle to the before last
projection angle, i.e., in your case
209.609216488925-11.6067737022482
so it's a span of 199 degrees and your cone angle is indeed too large.
Like I said, this part of RTK is perfectible and there is no way to
change this but change the code.
However, the source of artefacts might be something else. On simulated
data, I tried:
rtkprojectshepploganphantom --like original_proj.mhd -g
geometry_parker_corr.xml -o proj.mha
rtkfdk -p . -r proj.mha -o fdk.mha -g geometry_parker_corr.xml
and the result is not that bad. What do you think? Can you show us a
snapshot if sg's wrong in your opinion?
Simon
On 09/12/2015 11:01, Shiras Abdurahman wrote:
> Dear Simon,
>
> I am attaching the mhd files of projections.
>
> With regards,
> Shiras
>
> On Tue, Dec 8, 2015 at 6:17 PM, Simon Rit
> <simon.rit at creatis.insa-lyon.fr
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
> Hi,
> The geometry files look ok to me. What is the projection
> information? If you're still getting the same message as before, I
> think it's because you don't have enough data. If you send the mhd
> file of the projections (just the mhd, not the raw data), I can
> try to test it on simulated data to let you know my feeling.
> Simon
>
> On Tue, Dec 8, 2015 at 5:41 PM, Shiras Abdurahman
> <shiraska at gmail.com <mailto:shiraska at gmail.com>> wrote:
>
> Dear Simon,
>
> I tried this option and unfortunately it did not work. I added
> zero projections and modified geometry files. However, I am
> getting same artifacts in the volume. Voxel values changed a
> little bit that indicates during backprojection it still
> considers extreme projections. I am also getting an output
> message same as before.
>
> I am attaching geometry files.
>
> With regards,
> Shiras
>
> On Tue, Dec 8, 2015 at 10:15 AM, Simon Rit
> <simon.rit at creatis.insa-lyon.fr
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
> So calling AddProjection before and after the loop with an
> adequate gantry_angle should work.
> Simon
>
> On Tue, Dec 8, 2015 at 9:52 AM, Shiras Abdurahman
> <shiraska at gmail.com <mailto:shiraska at gmail.com>> wrote:
>
> Drear Simon,
>
> I generate the geometry with system geometry
> parameters and using AddProjection method.
>
> Here is the code
>
>
> rtk::ThreeDCircularProjectionGeometry::Pointer
> rtk_sys_geometry_;
> rtk_sys_geometry_ =
> rtk::ThreeDCircularProjectionGeometry::New();
> for (uint16_t proj_index = 0; proj_index <
> num_projections_; proj_index++)
> {
> rtk_sys_geometry_->AddProjection(rtk_geom_params_.at(proj_index).sid_mm,
> rtk_geom_params_.at(proj_index).sdd_mm,
> rtk_geom_params_.at(proj_index).gantry_angle_deg,
> rtk_geom_params_.at(proj_index).proj_offset_x_mm,
> rtk_geom_params_.at(proj_index).proj_offset_y_mm,
> rtk_geom_params_.at(proj_index).out_plane_angle_deg,
> rtk_geom_params_.at(proj_index).in_plane_angle_deg,
> rtk_geom_params_.at(proj_index).src_offset_x_mm,
> rtk_geom_params_.at(proj_index).src_offset_y_mm);
> }
>
> And then write to xml file.
>
> Shiras
>
>
>
> On Tue, Dec 8, 2015 at 9:23 AM, Simon Rit
> <simon.rit at creatis.insa-lyon.fr
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
> Hi,
> rtkfdk.cxx just read the geometry from a file so
> the best is to modify the geometry file. How do
> you generate the geometry?
> For example, if you use rtksimulated geometry,
> let's say that you were using:
> rtksimulatedgeometry -n 200 -a 200 -o g.xml
> then you'll have to replace it with
> rtksimulatedgeometry -n 202 -a 202 -o g.xml -f -1
> Don't forget to add dummy projection at the
> beginning and the end. If you use a more complex
> geometry, maybe SimpleRTK
> <http://wiki.openrtk.org/index.php?title=SimpleRTK> can
> be helpful (I'd use that) or you'd have to modify
> the cxx code to add these additional projections
> in the geometry and the projection stack.
> Simon
>
>
> On Tue, Dec 8, 2015 at 8:51 AM, Shiras Abdurahman
> <shiraska at gmail.com <mailto:shiraska at gmail.com>>
> wrote:
>
> Dear Simon,
>
> Thanks a lot for the reply. Can you please
> inform me how can I set where the arc starts?
> Do I need to modify geometry also?
> If you can point the line of code rtkfdk.cxx,
> it will be really helpful.
>
> With regards,
> Shiras
>
> On Tue, Dec 8, 2015 at 7:56 AM, Simon Rit
> <simon.rit at creatis.insa-lyon.fr
> <mailto:simon.rit at creatis.insa-lyon.fr>> wrote:
>
> Dear Shiras,
> Yes, for practical reasons the first and
> the last projections are set to 0 and the
> arc used in the Parker weighting starts
> between the first two projections and ends
> between the lasts two projections. There
> is a simple solution: add a projection at
> the beginning and the end of the arc,
> which can contain any pixel values but
> should be set where you want this arc to
> start. In the future, I think someone
> should once take the time to correct this
> but I haven't so far. I'll keep you posted
> on the mailing list when it's corrected.
> Simon
>
> On 07/12/2015 12:04, Shiras Abdurahman wrote:
>> Hi all,
>>
>> I am trying to reconstruct a volume from
>> projection data generated with C-arm CT.
>> There are 248 projections with an angular
>> range of 199 degree. Technically, parker
>> weighting should run without any
>> problems. However, I am getting an output
>> message that "You do not have enough data
>> for proper parker weighting". After
>> parker weighting, the two extreme
>> projections (projection number 1 and 248)
>> were completely zero and thus
>> reconstructed volume contained artifacts.
>> When I increased the angular range, this
>> problem did not happen. How can I solve
>> this problem without increasing angular
>> range? Is there any threshold constant
>> that I can change in command line or in
>> my code?
>>
>> I really appreciate any help you can provide.
>>
>> With regards,
>> Shiras
>>
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> <mailto:Rtk-users at public.kitware.com>
>> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
>
>
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.creatis.insa-lyon.fr/pipermail/rtk-users/attachments/20151218/04fb9d58/attachment.htm>
More information about the Rtk-users
mailing list