[Gate-users] Further documentation of output images created by the FixedForcedDetection Actor

Fri Sep 2 12:24:25 CEST 2016

On 02/09/2016 11:53, Lukas Gromann wrote:
> Hi Simon,
>
> thanks for your fast reply, this helps me already a lot. Indeed I read 
> those parts in the wiki and had also a short look at the papers 
> mentioned.
>
> Especially the following questions still arise for me:
> - What are the „signals“ in primary, total, compton etc? Are these 
> detection probabilities? Photon counts? Or total recorded 
> Photon-Energies per pixel, or is this converted to some arbitrary 
> ADU-values?
There is a detector response curve that will set this. This is a text 
file in which the first column is the incoming photon energy (in MeV) 
and the second column is the detected signal. It's used both in the 
Monte Carlo and the fixed forced detection examples, I first describe it 
for Monte Carlo where you have one photon arriving on the pixel at a 
time. If you don't set it, it will integrate the energy of the incoming 
photons, which would be similar to setting it to a ramp:
0 0
1 1
Note that the values are linearly interpolated.

The other option is to do a photon counting, so to add 1 regardless of 
the energy:
0 1
1 1

You can also set a much more complex (but more realistic) function, as 
described in [Roberts et al, PMB, 2008] 
<dx.doi.org/10.1088/0031-9155/53/22/003> which we recently used in 
[Vilches-Freixas et al, Med Phys, 2016] 
<http://dx.doi.org/10.1118/1.4961400>. I have enclosed an example.

Now, for fixed forced detection, the final value is also multiplied by 
the probability of having a photon with that energy in this pixel since 
this is what FFD computes.

> - I guess this is related to the energy-response of the detector? 
>  Also here the example provides some basic responseDetector.txt, but 
> the Syntax is not clear to me.
> - In the example Code, there is an option called 
> „/gate/actor/ffda/energyResolvedBinSize        0 keV“, which is not 
> mentioned in the wiki at all. If I would set this Value to 1keV, would 
> I create a Photon counting detector with 120 energy bins? How would 
> the Output look like? 120 images each for „compton“ and "primary“?
Yes, these are recent (unreleased) dev. If you set this to a non 0 
value, instead of storing 2D projection images, it stores 3D projection 
images where the third dimension is the energy. There is still one 
projection only per gantry angle. Indeed, if your max spectrum energy, 
it would create 120 energy bins with a perfect energy resolved detector.
>
>
>
> I would therefore suggest to add at least the following lines to the 
> documentation:
>>
>> All contributions are summed in total which can be decomposed in 
>> primary+secondary. Secondary (same as scatter) can itself be 
>> decomposed in compton+rayleigh+fluorescence. flatfield is available 
>> to compute the measured primary signal if there is no object, this is 
>> useful for CT to apply the beer Lambert law. attenuation is 
>> ln(flatfield/primary) to get the line integral, i.e., the input of 
>> most CT reconstruction algorithms.
>>
>
Yep, will do + what I just say. I suggest to continue the discussion 
when something is not clear and I'll summarize soon on the wiki. Keep 
asking!
>
> Thanks,
>
> Lukas
>
> ----------------------------------------------------
> Lukas Gromann
>
> Lehrstuhl für Biomedizinische Physik (E17)
> Technische Universität München
> Boltzmannstrasse 11
> 85748 Garching
>
> Lukas.Gromann at TUM.de <mailto:Lukas.Gromann at TUM.de>
>
> Tel.: 089-289/10905
> Mobil: 017629718306
>
> Am 02.09.2016 um 11:02 schrieb Simon Rit 
> <simon.rit at creatis.insa-lyon.fr <mailto:simon.rit at creatis.insa-lyon.fr>>:
>
>> Hi,
>>
>> I assume you've read
>>
>> http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.2:Readout_parameters_for_Radiotherapy_applications:_Actors#Fixed_Forced_Detection_CT?
>>
>> It's scarce but there are a bunch of references we suggest to 
>> understand the technique. The numbers are the expected signal in the 
>> image. All contributions are summed in total which can be decomposed 
>> in primary+secondary. Secondary (same as scatter) can itself be 
>> decomposed in compton+rayleigh+fluorescence. flatfield is available 
>> to compute the measured primary signal if there is no object, this is 
>> useful for CT to apply the beer Lambert law. attenuation is 
>> ln(flatfield/primary) to get the line integral, i.e., the input of 
>> most CT reconstruction algorithms.
>>
>> An alternative is to do pure monte carlo, see monteCarloCT.mac in the 
>> same folder. I guess there are other options in Gate but I don't know 
>> all the CT options in Gate. Please let me know if you find some!
>>
>> Hope this helps and let us know if/how we should complete the "doc",
>>
>> Simon
>>
>>
>> On 02/09/2016 09:49, Lukas Gromann wrote:
>>> Dear all,
>>>
>>> I am currently learning how to use Gate for my PHD project in 
>>> medical x-rax imaging.
>>>
>>> I would like to simulate the Compton scatter fraction in a simple 
>>> Thorax x-ray. I started by using the 
>>> example_CT/fixedForcedDetectionCT, which looks like the thing I am 
>>> looking for. Unfortunately I cannot find any documentation, what is 
>>> actually the content of the outputfiles created by the 
>>> FixedForcedDetection actor. What does the numbers in the various 
>>> images represent? What is the purpose of the flatfield file?
>>> Any kind of additional documentation/information would be very welcome!
>>>
>>> On the other hand, is there maybe a much better approach to 
>>> determine Compton scatter fractions in my images than using the FFD 
>>> actor?
>>>
>>> Thanks for your help,
>>>
>>> Lukas
>>>
>>> ----------------------------------------------------
>>> Lukas Gromann
>>>
>>> Lehrstuhl für Biomedizinische Physik (E17)
>>> Technische Universität München
>>> Boltzmannstrasse 11
>>> 85748 Garching
>>>
>>> Lukas.Gromann at TUM.de <mailto:Lukas.Gromann at TUM.de>
>>>
>>> Tel.: 089-289/10905
>>> Mobil: 017629718306
>>>
>>>
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>> On 02/09/2016 09:49, Lukas Gromann wrote:
>>> Dear all,
>>>
>>> I am currently learning how to use Gate for my PHD project in 
>>> medical x-rax imaging.
>>>
>>> I would like to simulate the Compton scatter fraction in a simple 
>>> Thorax x-ray. I started by using the 
>>> example_CT/fixedForcedDetectionCT, which looks like the thing I am 
>>> looking for. Unfortunately I cannot find any documentation, what is 
>>> actually the content of the outputfiles created by the 
>>> FixedForcedDetection actor. What does the numbers in the various 
>>> images represent? What is the purpose of the flatfield file?
>>> Any kind of additional documentation/information would be very welcome!
>>>
>>> On the other hand, is there maybe a much better approach to 
>>> determine Compton scatter fractions in my images than using the FFD 
>>> actor?
>>>
>>> Thanks for your help,
>>>
>>> Lukas
>>>
>>> ----------------------------------------------------
>>> Lukas Gromann
>>>
>>> Lehrstuhl für Biomedizinische Physik (E17)
>>> Technische Universität München
>>> Boltzmannstrasse 11
>>> 85748 Garching
>>>
>>> Lukas.Gromann at TUM.de <mailto:Lukas.Gromann at TUM.de>
>>>
>>> Tel.: 089-289/10905
>>> Mobil: 017629718306
>>>
>>>
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>> _______________________________________________
>> Gate-users mailing list
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>> <mailto:Gate-users at lists.opengatecollaboration.org>
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
>
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