[Rtk-users] RTK code correction

[Simon Rit]

Hi Uffe,
I have committed some changes that should take care of the scatter
correction bug
https://github.com/SimonRit/RTK/commit/984564ab6d445cf1ff6c625eabca8cc2caba4b7e
The scatter to primary ratio is still set to 0 by default. I'll try to
find a way to pass such parameters from the command line of rtk
applications but in the mean time, you may want to test it. Feedback
is appreciated.
Thanks again for reporting this,
Simon

On Sun, Sep 15, 2013 at 10:40 PM, Simon Rit
<simon.rit at creatis.insa-lyon.fr> wrote:
> 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
>>>