[Gate-users] Dose Actor Voxels?

Tue Jan 15 21:52:47 CET 2019

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>
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>
> *Sent:* Tuesday, January 15, 2019 3:38 PM
> *To:* Josh Knowland <jknowland at lucernodynamics.com>
> *Cc:* 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> 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
> *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>
> *Sent:* Tuesday, January 15, 2019 11:46 AM
> *To:* Ben Kopchick <kopchickbp at email.gwu.edu>
> *Cc:* Josh Knowland <jknowland at lucernodynamics.com>;
> 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> 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> 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' <
> 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> *On
> Behalf Of *Josh Knowland
> *Sent:* Tuesday, January 15, 2019 11:03 AM
> *To:* 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>
> *Sent:* Tuesday, January 15, 2019 10:22 AM
> *To:* Josh Knowland <jknowland at lucernodynamics.com>;
> 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>
> on behalf of Josh Knowland <jknowland at lucernodynamics.com>
> *Sent:* January 14, 2019 2:53:48 PM
> *To:* 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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> --
>
> 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"
> _________________________________
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

-- 
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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