[Rtk-users] RTK calculating attenuation from Varian projection

[Simon Rit]

Hi,
Thanks for the feeback. I don't know any users that actively use
Varian projection images. I will put a Catphan dataset online soon
that has been provided by Greg Sharp and I'll try to adjust
reconstructed values to linear attenuation. A filter to convert from
linear to attenuation to HU is rather easy to add if one feels it's
required.
Simon

On Mon, Nov 26, 2012 at 2:45 PM, Geoff Hugo <gdhugo at vcu.edu> wrote:
> Hi Simon and Andy,
>
> The ScaleFactor we use at VCU is a rough conversion from linear attenuation
> coefficient (the output of RTK) to something roughly around CT number
> (Hounsfield Units).  This is not a proper conversion, just a placeholder for
> now.  I'm not sure how useful the HNC-compatible version we have at VCU will
> be to the wider community, as HNC is not a generally available format and
> HND is the more common one.  Are there any other users of RTK that use
> Varian HNC format projections?
>
> Geoff
>
> On 11/23/12 6:35 AM, Andy Shieh wrote:
>
> Hi Simon,
>
> Just to let you know that the code works well!! Thanks!
>
> By the way, I've been contacting with A/Prof Geoff Hugo (I believe you know
> him?), and he mentioned that he's been putting quite some effort on making
> RTK compatible with Varian format (HNC mainly). He mentioned that for the
> Varian format, we usually read in the "Norm Chamber value" (It's usually
> around 300) from each HNC header, and calculate the CT number by
> log(NormChamberValue/Intensity) * ScaleFactor, where the ScaleFactor is
> around 10000. I'm not too sure about the details, but I believe he will
> discuss it with you soon when he has time!
>
> Cheers,
> Andy
>
>>
>>
>>
>> 2012/11/19 Simon Rit <simon.rit at creatis.insa-lyon.fr>
>>>
>>> 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
>>> >>> >
>>> >>> > _______________________________________________
>>> >>> > Rtk-users mailing list
>>> >>> > Rtk-users at openrtk.org
>>> >>> > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>> >>> >
>>> >>
>>> >>
>>
>>
>
>
>
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>
> --
> ------------------------------------
> Geoffrey D. Hugo, Ph.D.
> Assistant Professor
> Dept. of Radiation Oncology
> Virginia Commonwealth University
> gdhugo at vcu.edu