[Rtk-users] RTK calculating attenuation from Varian projection

[Simon Rit]

Hi Andy,
I have pushed a fix for the Varian raw to attenuation conversion. Let
me know if it meets what you've done. I will let you know if there is
any other improvement of the conversion in the future.
Simon

On Fri, Nov 9, 2012 at 9:03 AM, Simon Rit
<simon.rit at creatis.insa-lyon.fr> wrote:
> Hi Andy,
>
> On Thu, Nov 8, 2012 at 5:58 PM, Andy Shieh <hsieandy at gmail.com> wrote:
>> Hi Simon,
>>
>> Thank you. At the moment I'm just doing something similar to what you did
>> for the Elekta system - using a log_ref (I'm using HND_INTENSITY_MAX) and
>> minus the log of intensity plus one (I assume the plus one is to avoid
>> taking the log of zero?).
> Does it improve the results? You are welcome to share it if you feel
> that this is of interest for other people.
>
>>
>> Another few question:
>> 1. Are you doing any normalization after reconstruction or forward
>> projection?
> No. Assuming you have line integral of the attenuation as input of the
> reconstruction algorithm, you get the attenuation.
>
>  Are the negative values in the reconstructed images simply a
>> result of the ramp filtering?
> Probably. You can use rtkprojections to look at what is the input of
> the reconstruction algorithm.
>
>> 2. If I want to compare a reprojection from an image reconstructed using RTK
>> with the original projection, how should I make sure the normalization is
>> correct? i.e. should I plus/minus or multiply the  reprojected attenuation
>> before I use exponential and make it back to intensity values?
> You basically have to do the inverse formula to what you have done. An
> easy way of looking at what is going on with forward projections is to
> look at this example:
> http://wiki.openrtk.org/index.php/RTK/Scripts/ForwardProjection
>
>> 3. The rtkforward projections doesn't seem to work correctly when I'm
>> projecting using a geometry file containing several Projection (Angle). The
>> output mha file seems to "repeat" after a couple of projections instead of
>> showing all projections. I'm testing this on a Varian Half Fan geometry - it
>> works fine if I break the geometry file down into one each for each
>> projection angle and do the forward projection separately. I can send you a
>> reprojection mha file if my description is unclear to you.
> I works for me. Would you be able to fill in a bug report
> (http://bug.openrtk.org/) with an example? You can generate volumes
> and projections with rtkdrawgeometricphantom and
> rtkprojectgeometricphantom.
> Simon
>
>>
>> Thanks Simon!!
>>
>> Cheers,
>> Andy.
>>
>>
>>
>> 2012/10/24 Simon Rit <simon.rit at creatis.insa-lyon.fr>
>>>
>>> Hi Andy,
>>> Yes you're right, I have actually noticed recently that but I have not
>>> worked a lot on Varian images because we don't have a Varian CBCT in
>>> Lyon. I only had a sub-sampled acquisition from Greg of a Catphan that
>>> I used to roughly check the geometry. As far as I can remember, when I
>>> wrote this piece of code, I tried to use the same code as Plastimatch
>>> but I could well have done it wrongly. I'm actually waiting for a new
>>> complete Catphan acquisition from Greg to correct for this but if you
>>> already have a patch to suggest or a set of images to send, feel free
>>> to do it.
>>> Thanks,
>>> Simon
>>>
>>> On Tue, Oct 23, 2012 at 2:48 PM, Andy Shieh <hsieandy at gmail.com> wrote:
>>> > Hi Simon,
>>> >
>>> > I was looking at "rtkVarianObiRawImageFilter.h", and realized that the
>>> > attenuation is calculated from the projection image simply via a
>>> > negative
>>> > transformation (1-Intensity/HND_MaxIntensity).
>>> > Is it usually the way this is done, and is there any reason for doing
>>> > this?
>>> > I would have thought attenuation should be calculated from intensity via
>>> > logarithm (since I=I_0 exp(-mu x)).
>>> > Thanks!!
>>> >
>>> > Cheers,
>>> > Andy
>>> >
>>> > _______________________________________________
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>>> > Rtk-users at openrtk.org
>>> > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>> >
>>
>>