[Rtk-users] RTK code correction

[Simon Rit]

Hi Uffe,
I think you're right but I must take the time to look into it
carefully. The algorithm is that of Boellaard, no doubt about it. But
I think I should have split
rtkElektaSynergyRawToAttenuationImageFilter in two and apply it in
betwee. I'll try to fix that asap but I have a very busy week. I'll
keep you posted...
Simon

On Fri, Sep 13, 2013 at 10:10 AM, Uffe Bernchou <Uffe.Bernchou at rsyd.dk> wrote:
>
> Dear Simon,
>
> Thank you very much for your reply. It will help me a lot.
>
> I did try to play a little with the BoellaardScatterCorrection. Setting m_ScatterToPrimaryRatio to 0.2 (I have been informed that this is the value used clinically in XVI) gives awful images. I think there might be something generally wrong with the implementation, but I could definitely be incorrect.
>
> The raw .his images from XVI have high values when the beam is blocked and low values when unblocked. As far as I can see, the images in BoellaardScatterCorrectionImageFilter still have this format. If this is true, the code
>
> ***
> for(unsigned int i=0; i<npixelPerSlice; i++)
>       {
>       smallestValue = std::min(smallestValue, (double)itInSlice.Get() );
>       if(itInSlice.Get()>=m_AirThreshold)
>         {
>         averageBehindPatient += itInSlice.Get();
>         }
>       ++itInSlice;
>       }
> averageBehindPatient /= npixelPerSlice;
> ***
>
> correctly finds the average pixel value behind the patient. Afterwards the scatter correction is calculated:
>
> ***
> // Compute constant correction
> double correction = averageBehindPatient * m_ScatterToPrimaryRatio;
>
> // Apply non-negativity constraint
> if(smallestValue-correction<m_NonNegativityConstraintThreshold)
>    correction = smallestValue - m_NonNegativityConstraintThreshold;
> ***
>
> However, then the correction is subtracted:
>
> ***
> // Remove constant factor
> for(unsigned int i=0; i<npixelPerSlice; i++)
>   {
>   itOut.Set( itIn.Get() - correction );
>   ++itIn;
>   ++itOut;
>   }
> ***
>
> But as far as I understand, this cannot be right when the images have the format mentioned above. It would add more scatter to the projection instead of subtracting. I think the non-negativity constraint also is fault by the same argument.
>
> Maybe I'm missing something and would be happy to be proven wrong :-)
>
> Best regards,
> Uffe
>
>
>
> -----Oprindelig meddelelse-----
> Fra: simon.rit at gmail.com [mailto:simon.rit at gmail.com] På vegne af Simon Rit
> Sendt: 13. september 2013 09:32
> Til: Uffe Bernchou
> Cc: Carsten Brink; Rune Slot Thing; rtk-users at openrtk.org
> Emne: Re: RTK code correction
>
> Hi Uffe,
> Thanks for your email. Please prefer the mailing list for questions of
> general interest, you might get quicker answer!
> It is correct that BoellaardScatterCorrectionImageFilter it not
> activated. But it is in place. So let me try to describe how that
> works:
> - many RTK programs use the filter rtkProjectionsReader.h to read raw
> data and convert them to attenuation. These two steps correspond to
> filters that are scanner dependent. The pointers to these filters are
> stored in m_RawDataReader and m_RawToProjectionsFilter.
> - the raw to attenuation conversion of Elekta Synergy is
> rtkElektaSynergyRawToAttenuationImageFilter.h. This filter is a
> so-called mini-pipeline filter, i.e., a pipeline of filters. One of
> them is the BoellaardScatterCorrection.
> - you should have a look at the implementation of this filter. You
> will notice that you have some parameters to set. One of them is the
> m_ScatterToPrimaryRatio. It speaks for itself I think. Right now, it
> is set to 0 so there is no scatter correction. But you can modify it
> to test the scatter correction. FYI, it was by default set to 0.33 in
> the first versions of XVI (it might have been lowered since because we
> had observed that it was not always ideal but I did not check). There
> is no mechanism to set it from the command line of rtkfdk yet but that
> could quite easily be done.
> Simon
>
> On Wed, Sep 11, 2013 at 8:36 PM, Uffe Bernchou <Uffe.Bernchou at rsyd.dk> wrote:
>> Dear Simon,
>>
>>
>>
>> I'm still very curious as to whether a simple solution to correct for
>> scatter is attempted in rtkfdk. I can see that the procedure for scatter
>> correction used in XVI is implemented in
>> BoellaardScatterCorrectionImageFilter, but this code does not seem to be
>> used anywhere when running rtkfdk. However, it could just be me getting lost
>> in the code J
>>
>>
>>
>> It would help me a lot if you could inform me as to whether any solution
>> scatter subtraction is done when running rtkfdk.
>>
>>
>>
>> Best Regards
>>
>> Uffe
>>