[Gate-users] Dose Actor Voxels?

Tue Jan 15 21:54:44 CET 2019

Yes, I saw that, but I’m using tessellated geometry right now. I’d have to generate MHD files for the models – which might be worth doing.

Thanks!
Josh

From: David Sarrut <David.Sarrut at creatis.insa-lyon.fr>
Sent: Tuesday, January 15, 2019 3:53 PM
To: Josh Knowland <jknowland at lucernodynamics.com>
Cc: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Dose Actor Voxels?

yes, note that a new DoseByRegion option is now available :
http://wiki.opengatecollaboration.org/index.php/Users_Guide:Tools_to_Interact_with_the_Simulation_:_Actors#Dose_by_regions
https://github.com/OpenGATE/GateContrib/tree/master/dosimetry/doseByRegions

it may help for total dose in a organ

On Tue, Jan 15, 2019 at 9:48 PM Josh Knowland <jknowland at lucernodynamics.com<mailto:jknowland at lucernodynamics.com>> wrote:
Thank you David, seeing the code did help.

So dose output is always per voxel. If I’m understanding correctly, then to find total dose to an organ, I would need to average all the voxels within that organ.
I believe an alternative would be to use Edep from GATE along with the calculated volume of the organ and its density to calculate dose myself.

Thanks,
Josh

From: David Sarrut <David.Sarrut at creatis.insa-lyon.fr<mailto:David.Sarrut at creatis.insa-lyon.fr>>
Sent: Tuesday, January 15, 2019 3:38 PM
To: Josh Knowland <jknowland at lucernodynamics.com<mailto:jknowland at lucernodynamics.com>>
Cc: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Dose Actor Voxels?

no averaging: edep is deposited at a given point position, then summed with all other edep in the voxel that include this point position. The output of the DoseActor is edep (or dose) in each voxel volume. Those voxel are the ones defined by the user in the DoseActor, sometimes called dosels or scoring voxels (NOT the voxels of an underlying CT image for example).

More detail in the source code :
https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateDoseActor.cc#L463

or line : https://github.com/OpenGATE/Gate/blob/develop/source/digits_hits/src/GateDoseActor.cc#L549

David

On Tue, Jan 15, 2019 at 9:30 PM Josh Knowland <jknowland at lucernodynamics.com<mailto:jknowland at lucernodynamics.com>> wrote:
All, I have made progress in using the dose output from the doseActor, but I still have a question about the overall use of it.

If I have my 100mm x 100mm x 100mm cube of water and let’s say 1 Joule of energy is deposited into the first 50mm of one side. The dose for the entire cube would be 1J/1kg = 1 Gy.

Now, if I split the cube into two voxels, all the energy deposits into the first voxel and none into the second. Now the dose is:
1J/.5kg + 0J/.5kg = 2Gy+0Gy. Obviously, this sum of doses needs to be averaged over all the voxels.

My question is, is this averaging already done by Gate in the doseActor? And if so, does it use all the voxels in the doseActor or only those which fall within the orgam geometry?

I do get different total dose for different voxel sizes, so I fear it is averaging over all the voxels.

Thank you,
Josh

From: Josh Knowland
Sent: Tuesday, January 15, 2019 12:05 PM
To: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: RE: [Gate-users] Dose Actor Voxels?

Thank you David,

I think I am finally making sense of it. The problem, I believe, was that I was attempting to do this: (sum of all Edep) / (sum of all mass). It is not the same as calculating the dose for each voxel and then adding those.

I am getting agreement in calculations now, thank you!

Josh

From: David Sarrut <David.Sarrut at creatis.insa-lyon.fr<mailto:David.Sarrut at creatis.insa-lyon.fr>>
Sent: Tuesday, January 15, 2019 11:46 AM
To: Ben Kopchick <kopchickbp at email.gwu.edu<mailto:kopchickbp at email.gwu.edu>>
Cc: Josh Knowland <jknowland at lucernodynamics.com<mailto:jknowland at lucernodynamics.com>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Dose Actor Voxels?

Hello

The dose actor do not consider anything except edep and mass in the given voxel, whatever the volume.

Dose is edep divided by mass. Consider edep to better understand your results ...

HTH,
David

Le mar. 15 jans. 2019 à 17:34, Ben Kopchick <kopchickbp at email.gwu.edu<mailto:kopchickbp at email.gwu.edu>> a écrit :
Hi Josh,

In your original test, if you average the dose of the 1000 voxels do you get the same dose as the single voxel? I believe this should be the test as Dose (Gy) is dependent on the mass of the material.

Best,

Benjamin Kopchick

On Tue, Jan 15, 2019 at 11:25 AM Josh Knowland <jknowland at lucernodynamics.com<mailto:jknowland at lucernodynamics.com>> wrote:
To continue what I have found –

The correct dose is not simply dividing by the total number of voxels in the doseActor. In fact, I have to divide by the total number of voxels in the union of the doseActor and the geometry volume its attached to.

For instance, if I make my cube of water 100mm on a side, but make the doseActor 125mm on a side, I will only register dose within the volume of the cube. This makes sense – I should register zero dose for those voxels outside of the water cube.

However, during dose calculation, the doseActor multiplies by the number of voxels that fell within the water cube. When using complex geometry from STL files, I can’t know this number.

It seems the calculation would be fine if the doseActor is contained completely within your geometry, but how can you encompass an entire geometry (say, a liver organ modeled in STL) using the rectangular solid doseActor? I can’t know exactly how many doseActor voxels actually fall within the liver.

From: Josh Knowland
Sent: Tuesday, January 15, 2019 11:06 AM
To: 'gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>' <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: RE: Dose Actor Voxels?

Sorry, I had a typo. I meant:

  *   Dose from doseActor seems to always multiply by the number of doseActor voxels. If I sum the dose output and then divide by the number of voxels, I get the same as if I calculate dose from Edep.

From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> On Behalf Of Josh Knowland
Sent: Tuesday, January 15, 2019 11:03 AM
To: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Dose Actor Voxels?

Hi Matthew, thank you for the reply.

Here is what I have done to try to verify the calculations:

  *   Simulation of 1 liter of water hit with F18 positrons.
  *   Calculated dose three ways:

     *   Summing Edep from Singles output and converting to Gray.
     *   Summing Edep from doseActor and converting to Gray.
     *   Summing dose from doseActor (already Gray).

  *   Edep from Singles and summed Edep from doseActor always agree.
  *   Dose from doseActor seems to always divided by the number of doseActor voxels. If I sum the dose output and then multiply by the number of voxels, I get the same as if I calculate dose from Edep.

Can anyone explain this? When the dose map is already divided by voxel, why can’t I just sum all the voxels? I get the same results using VolumeWeighting or MassWeighting (of course, I’m using 1 liter of water, so that’s the same.)

Thank you all,
Josh

From: Matthew Strugari <matthew.strugari at dal.ca<mailto:matthew.strugari at dal.ca>>
Sent: Tuesday, January 15, 2019 10:22 AM
To: Josh Knowland <jknowland at lucernodynamics.com<mailto:jknowland at lucernodynamics.com>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: Dose Actor Voxels?

Hi Josh,

I am not entirely familiar on the behaviour of the doseActor, but it appears that the output dose is given as the dose per voxel. Hence, the same dose is deposited after integration in each case.

Matthew

________________________________
From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> on behalf of Josh Knowland <jknowland at lucernodynamics.com<mailto:jknowland at lucernodynamics.com>>
Sent: January 14, 2019 2:53:48 PM
To: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] Dose Actor Voxels?

All,

Can you explain how the voxel size and number impacts the calculated dose by the doseActor?

I have simulated a 1 liter cube of water containing 0.01 mCi of 18F positrons. When I enable the doseActor using 1000 voxels each 1cm^3, I get a total of 2.43E-05 Gy. However, if I enable the doseActor using only 1 voxel of size 10cm^3, I get a dose of 2.43E-02 Gy.

I get the same total energy deposited no matter the voxel size and number, why not dose?
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CREATIS, UMR CNRS 5220, Inserm U1206
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David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U1206
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
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--
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U1206
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
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