[Gate-users] Potential bug in units to materials conversion

[Matthew Strugari]

Hi David,

No luck with "buildAndDumpLabeledImage". I implemented as
/gate/phantom/geometry/buildAndDumpLabeledImage             data/Cropped_kidneyContour_binary.mhd
but there was no associated output.

I assume this is the correct usage as suggested by the --qt viewer.

Regards,
Matthew

________________________________
From: David Sarrut <David.Sarrut at creatis.insa-lyon.fr>
Sent: March 2, 2020 11:56 AM
To: Matthew Strugari <matthew.strugari at dal.ca>; David Boersma <david.boersma at medaustron.at>
Subject: Re: [Gate-users] Potential bug in units to materials conversion

Hi Matthew,

quick idea: try "buildAndDumpLabeledImage" to see what happens ...

DavidB : any idea ?

Thanks,
David

On Mon, Mar 2, 2020 at 4:33 PM Matthew Strugari <matthew.strugari at dal.ca<mailto:matthew.strugari at dal.ca>> wrote:
Hi everyone,

As a followup to my previous email, it appears that the bug affects voxelized simulation results. After allowing the simulation to run to completion, the dose distribution due to 40 million Y-90 primaries does not show any back-scatter effects at the air-water interface. I have attached an image which highlights a couple regions showing the extension of dose into "air". The dose decreases smoothly with distance from the source despite crossing the boundary.

I use the following lines to define my voxelized phantom:
/gate/world/daughters/name                                  phantom
/gate/world/daughters/insert                                ImageNestedParametrisedVolume
/gate/phantom/geometry/setImage                             data/Cropped_kidneyContour_binary.mhd
/gate/phantom/geometry/TranslateTheImageAtThisIsoCenter     0 0 0 mm
/gate/phantom/geometry/setRangeToMaterialFile               data/KidneyAttenuationRange.dat

I have also changed the attenuation range to overlap with values near 0 and 1 in case of any floating point errors to no avail. If anyone sees any mistakes in my phantom definition or has encountered similar issues, please let me know. I am not sure what to do about this.

Regards,
Matthew

________________________________
From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> on behalf of Matthew Strugari <matthew.strugari at dal.ca<mailto:matthew.strugari at dal.ca>>
Sent: February 28, 2020 12:43 PM
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: [Gate-users] Potential bug in units to materials conversion

Dear gate-users,

There appears to be an issue when defining the associated material for each voxel in an image. I have loaded a binary image with the units to materials conversion defined in a AttenuationRange.dat file:
2
0 0 worldDefaultAir
1 1 Water
I have also set the world material as worldDefaultAir resulting in a total of two defined materials throughout my entire simulation. When executing my macro, there is a message stating that 3 materials are in the image:
[Volume-1]  Number of different materials in the image data/Cropped_contour_binary.mhd : 3
[Physic-1]
[Physic-1]  ----------------------------------------------------------
[Physic-1]                      Ionization potential
[Physic-1]   - worldDefaultAir defaut value: I = 85.7031 eV
[Physic-1]   - Air defaut value: I = 85.6694 eV
[Physic-1]   - Water defaut value: I = 68.9984 eV
[Physic-1]  ----------------------------------------------------------
Has anyone else noticed this issue? I don't know if it's possible to verify what voxels are assigned to what material. It would be nice to see the total number of voxels assigned to a given material at run time.

Best,

Matthew


--

Matthew Strugari

Biomedical Translational Imaging Centre - BIOTIC,
5890 University Ave,
Halifax, NS, B3K 6R8

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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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