[Rtk-users] Parker weighting

[Shiras Abdurahman]

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>
> 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> 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>
>>> 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> 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>
>>>>> 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> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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