[Rtk-users] Issues using PhaseGatingImageFilter

[Chao Wu]

Hi Cyril,

Thanks for your explanation very much. I thought the phase numbers
would be integers like 0, 1, 2,... so the three centers seem to be
strange. If all are between 0 and 1 then the -1 and +1 centers for
wrapping make sense. I will look further into your suggestions about
gated FDK and try different things. Thanks again.

Regards, Chao

2015-01-15 15:52 GMT+01:00 Cyril Mory <cyril.mory at creatis.insa-lyon.fr>:
> Hi Chao,
>
> It can be confusing indeed, and I should have added documentation. It is a
> quite common way to perform gating in the cardiac tomography community, but
> not in IGRT.
> PhaseGatingImageFilter computes gating weights that depend on the distance
> between a projection's phase and the target phase (both expressed as floats
> in [0; 1[ ), and a window shape. The window's shape describes how the gating
> weight decreases when the distance between a projection's phase and the
> target phase increases.
>
> If the window is rectangular, then the weights are binary. If it is
> triangular, they decrease linearly with distance. You can imagine all sorts
> of window shapes (cosine-squared, bump, ...)
>
> The gating method you describe in
>
> To reconstruction phase N, shouldn't only projections acquired within window
> N be used?
>
> corresponds to a rectangular window. If you are reconstructing 10 frames,
> each one covers 10% of the cycle, and you should use a gating window of
> width 0.1 centered on 0.05 for the first frame, 0.15 for the second frame,
> etc...
>
> Now, about the three centers: if you are reconstructing either the very
> beginning or the very end of the cycle, with a wide window, you end up
> needing to wrap around the cycle. For example, if you reconstruct phase 0.9
> with window width 0.3, the non-zero weights span [0.75; 1.05]. And you want
> them to span [0; 0.05] U [0.75; 1[ instead. Again, this is never used in
> IGRT, but happens in cardiac.
>
> Finally, about the Parker weighting: there doesn't seem to be a "good" way
> to combine gating and Parker weighting. I have used PhaseGatingImageFilter
> only in SART and ADMM_TV, for which Parker weighting is unnecessary. If you
> want to perform gated FDK reconstructions with RTK, you could:
> - use PhaseGatingImageFilter with a rectangular window and extract the
> weights to get a list of projections to keep
> - use rtksubselect to construct a subset of projections, with only the ones
> you want to keep. It will extract the corresponding subgeometry for you
> - feed rtkfdk this subset of projections and subgeometry. It will apply
> Parker weights, assuming that gating hasn't removed too many projections at
> the beginning and at the end of your projection stack (because each
> projection removed reduces the total angular range of your "acquisition",
> and it may end up violating the "angularRange >= 180° + halfFanAngle"
> condition)
>
> If you can afford a SART reconstruction, then just use SART with the correct
> gating options. Note that if your gating window is tight, it should be much
> faster than a SART from the whole dataset. You can even do better, and
> initialize a gated SART with an ungated FDK, if you prefer some blur and no
> streaks to some streaks and no blur.
>
> I hope it helps, but do not hesitate to ask if you have more questions.
> Cyril
>
>
> On 01/15/2015 01:30 PM, Chao Wu wrote:
>>
>> Dear all,
>>
>> I am also looking at the PhaseGatingImageFilter. I think I am confused
>> by how the weights are computed in ComputeWeights().
>>
>> At line 83 and 84 the distance is calculated by
>> distance = vnl_math_min(fabs(m_GatingWindowCenter - 1 -
>> m_Phases[proj]), fabs(m_GatingWindowCenter - m_Phases[proj]));
>> distance = vnl_math_min(distance, vnl_math_abs(m_GatingWindowCenter +
>> 1.f - m_Phases[proj]));
>>
>> Then this distance seems to be the smallest distance between the phase
>> number and any of the three adjacent gating window centers.
>> Afterwards this distance is used for computing the weight based on the
>> window width and shape.
>> Why are three window centers used here? To reconstruction phase N,
>> shouldn't only projections acquired within window N be used?
>>
>> Another question is about using this filter in FDK. I was wondering
>> where's the best place to insert it. Before the
>> ParkerShortScanImageFilter or after?
>>
>> Thanks.
>>
>> Regards,
>> Chao
>>
>>
>> 2014-11-03 18:15 GMT+01:00 Simon Rit <simon.rit at creatis.insa-lyon.fr>:
>>>
>>> Great, it's been pushed.
>>> Simon
>>>
>>> On Mon, Nov 3, 2014 at 4:15 PM, Geoff Hugo <gdhugo at vcu.edu> wrote:
>>>>
>>>> Hi Simon,
>>>>
>>>> Yes, this was what I was thinking as well.  Thanks for implementing it,
>>>> it
>>>> worked fine.
>>>>
>>>> Geoff
>>>>
>>>> ------------------------------------
>>>> Geoffrey D. Hugo, Ph.D.
>>>> Associate Professor, Radiation Oncology
>>>> Director, Medical Physics Graduate Program
>>>> Virginia Commonwealth University
>>>> (804) 628 3457
>>>>
>>>>
>>>> On Nov 1, 2014, at 7:22 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
>>>> wrote:
>>>>
>>>>> Hi Geoff,
>>>>> I agree with your analysis, PhaseGatingImageFilter is not adequate for
>>>>> streaming, which is not surprising since Cyril uses it for iterative
>>>>> reconstruction and he typically works with the full stack of
>>>>> projections in RAM. I think there is a simple solution: move the
>>>>> update of the geometry from the GenerateData to the
>>>>> GenerateOutputInformation. That should solve the issue for you.
>>>>> Enclosed is a change suggestion, can you give it a try in the
>>>>> application you have built?
>>>>> I'll commit it if it helps,
>>>>> Simon
>>>>>
>>>>> On Fri, Oct 31, 2014 at 9:29 PM, Geoff Hugo <gdhugo at vcu.edu> wrote:
>>>>>>
>>>>>> I’m trying to use the PhaseGatingImageFilter class to reconstruct a
>>>>>> single
>>>>>> breathing phase volume and am running into some problems.  I’ve
>>>>>> incorporated
>>>>>> this class into an application similar to rtkfdk, putting it in the
>>>>>> pipeline
>>>>>> between ParkerShortScanImageFilter and
>>>>>> FDKConeBeamReconstructionFilter.
>>>>>> If
>>>>>> I run the application trying to select a subset of projections using
>>>>>> the
>>>>>> method SetGatingWindowCenter, I get a segmentation fault.  The fault
>>>>>> is
>>>>>> occurring due to allocation errors in
>>>>>> rtk::BackProjectionImageFilter::GenerateInputRequestedRegion.  It
>>>>>> appears
>>>>>> that since the geometry specific to the selected projections is
>>>>>> selected in
>>>>>> PhaseGatingImageFilter::GenerateData, there is a disconnect between
>>>>>> the
>>>>>> geometry size and projection stack size during
>>>>>> GenerateInputRequestedRegion
>>>>>> in the pipeline (pipeline OutputInformation shows the projection stack
>>>>>> size
>>>>>> is equal to the size of the selected breathing phase projections, but
>>>>>> the
>>>>>> geometry size is still the total number of (unsorted) projections).
>>>>>>
>>>>>> I can workaround this problem by calling
>>>>>> PhaseGatingImageFilter->Update(),
>>>>>> but I think this will break the streaming functionality?  Any easy
>>>>>> solutions
>>>>>> to this problem that will preserve streaming and let me run the full
>>>>>> pipeline with only one Update call?  My guess is I will need to move
>>>>>> the
>>>>>> geometry subselection to
>>>>>> PhaseGatingImageFilter::GenerateOutputInformation()
>>>>>> then call UpdateOutputInformation in the main application?
>>>>>>
>>>>>> Thanks,
>>>>>> Geoff
>>>>>>
>>>>>> ------------------------------------
>>>>>> Geoffrey D. Hugo, Ph.D.
>>>>>> Associate Professor, Radiation Oncology
>>>>>> Director, Medical Physics Graduate Program
>>>>>> Virginia Commonwealth University
>>>>>> (804) 628 3457
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Rtk-users mailing list
>>>>>> Rtk-users at public.kitware.com
>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>>>
>>>>> <rtkPhaseGatingImageFilter.txx>
>>>>
>>>>
>>>
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>
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> --
> Cyril Mory, Post-doc
> CREATIS
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