[Rtk-users] Reconstructing DICOM data

[Sreejith P P]

Hi,

Thank you so much for your support. It really helped. There was a problem
with my code creating Ankle.mha. I corrected it and got a decent result.

Cheers,
Sreejith

On Fri, Sep 23, 2022 at 6:09 PM Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Hi,
> Please, as I said before "To start with, I would make sure that everything
> outside the leg is at about 0 in your original Ankle CT data." I don't know
> the reason but your Ankle.mha file contains crazy values (Min: 9.43646e+07
> Max: 9.44526e+07). If I run
> rtkforwardprojections -g geoemtry.xml -i AnkleDICOM.mha -o test.mha --like
> Ankle.mha  -f CudaRayCast
> rtkfdk -g geometry.xml -o Output.mha -p . -r ^test.mha$ --dimension
> 512,512,245 --hardware cuda --hann 0.4 --hannY 0.4
> I have a more decent result. Remove or increase hann values to have a
> better spatial resolution.
> Cheers,
> Simon
>
> On Fri, Sep 23, 2022 at 9:36 AM Sreejith P P <sreejithputhettu at gmail.com>
> wrote:
>
>> Hi Simon,
>>
>> Thank you very much for your quick response.
>> As suggested, I have refined the Ankle Dicom data so that everything
>> outside the leg part is at 0. I got a fine projection 'Ankle.mha' after
>> doing that.
>> However, I didn't get much effect when I reconstructed it using rtkfdk. I
>> understand that projecting and reconstructing a CT image will necessarily
>> result in a loss of quality due to the multiple interpolations. But I
>> doubt, maybe something I am missing here can make it better. Could you have
>> a look at it, please?
>>
>> I used the following command for reconstruction.
>> *rtkfdk -g geometry.xml -o Output.mha -p . -r Ankle.mha --dimension
>> 512,512,245 --hardware cuda --hann 0.4 --hannY 0.4*
>>
>>  Ankle.mha
>> <https://drive.google.com/file/d/1M5hey85gQhh_gCC1dEvvr_EsXkRAOWm3/view?usp=drive_web>
>>  AnkleDICOM.mha
>> <https://drive.google.com/file/d/14qcXeN3IL_qHT3IbiJfMaQrTIPIPu81v/view?usp=drive_web>
>>  geoemtry.xml
>> <https://drive.google.com/file/d/105dwnd8dqgeE2d0qz9I9FPzH1t5b2gcc/view?usp=drive_web>
>>  output.mha
>> <https://drive.google.com/file/d/11COT9G6jzrHALPvUs8N4jnnZt9kuIMd3/view?usp=drive_web>
>>
>> Regards,
>> Sreejith
>>
>> On Tue, Sep 20, 2022 at 12:44 PM Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Hi,
>>> Your projections in Ankle.mha display a very large value in air. To
>>> start with, I would make sure that everything outside the leg is at about 0
>>> in your original Ankle CT data.
>>> Note that projecting and reconstructing a CT image will necessarily
>>> result in a loss of quality due to the multiple interpolations (during
>>> projection and backprojection). I would suggest to use fine pixels in the
>>> projections (e.g. --spacing .25) which you can bin during reconstruction
>>> (--binning 4,4).
>>> Simon
>>>
>>> On Mon, Sep 19, 2022 at 6:06 PM Sreejith P P <sreejithputhettu at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have created projections from 'Ankle' CT data using RTK (cuda
>>>> projection filter). It looks good to me.
>>>> After that, I tried rtkfdk application to reconstruct it.
>>>> I used the following command and got the attached output.
>>>>
>>>> *rtkfdk -g geometry.xml -o Output.mha -p . -r Ankle.mha --dimension
>>>> 512,512,245 --hardware cuda --pad 1.0 --hann 0.4 --hannY 0.4*
>>>>
>>>> Am I doing it correctly? If yes, I would like to know what I can do to
>>>> improve the result.
>>>>
>>>>  Ankle.mha
>>>> <https://drive.google.com/file/d/10ybESn9HoU9_LYDgaLUNYIf2BzTarQij/view?usp=drive_web>
>>>>  geometry.xml
>>>> <https://drive.google.com/file/d/1cTlvPld3iRNiRUW8HmnF29i_j6AmzaPW/view?usp=drive_web>
>>>>  Output.mha
>>>> <https://drive.google.com/file/d/1iI9V9TUIAKUMyfe-w6TTzFzS0DzvaGyn/view?usp=drive_web>
>>>>
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>>>>
>>>
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