[Rtk-users] Parker weighting
Shiras Abdurahman
shiraska at gmail.com
Mon Jan 11 09:34:58 EST 2016
Dear Simon,
I am sorry for the late reply. I also wish you a happy new year.
I will recheck if there is any error during generating projection images.
The projections are generated from a volume with our simulation tool.
However, I generated projections from the volume with rtkforwardprojections
and I re-reconstructed the volume with rtkfdk. I did not get any artifacts.
I will contact you soon, if I have some results.
Thank you very much for your help.
Shiras
On Fri, Dec 18, 2015 at 6:18 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:
> 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>
> 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>
>> 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>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>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>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>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>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 listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/rtk-users/attachments/20160111/3ae803cf/attachment-0009.html>
More information about the Rtk-users
mailing list