[Gate-users] Voxelized Source Problem

Christopher Watanabe chris.r.watanabe at gmail.com
Thu Nov 21 13:51:35 CET 2019 

Hello all,

After trying a good many things, I found something that works. The method
I'm producing my voxelized sources somehow sidesteps the need to shift the
volume in GATE at all. This I'm still looking into, but I guess it has
something to do with the .mhd file, as you will see in later comments. In
any case, the fix for the strange emissions going strictly in one direction
was solved by substituting "voxel" source emission definitions in the first
message with "thyroid_Phantom", or the name of the source, see *bold* text
below:



*# Inserting Voxelized Source/gate/source/addSource
                                    thyroid_Phantom
voxel/gate/source/thyroid_Phantom/*
*reader/insert
image/gate/source/thyroid_Phantom/*
*imageReader/translator/insert     linear/gate/source/thyroid_Phantom/*
*imageReader/linearTranslator/*
*setScale      1 Bq/gate/source/thyroid_Phantom/**imageReader/readFile
.data/thyroidPhantom/*
*thyroid_025mm.mhd/gate/source/thyroid_Phantom/*
*imageReader/verbose 1
/gate/source/thyroid_Phantom/**TranslateTheSourceAtThisIsoCen*
*ter      0 -2.0875 0 cm/gate/source/thyroid_Phantom/*

*dump                                       1/gate/source/thyroid_Phantom/*
*gps/particle                   gamma/gate/source/thyroid_Phantom/*
*gps/energytype              Mono/gate/source/thyroid_Phantom/*
*gps/monoenergy            140.5 keV/gate/source/thyroid_Phantom/*
*gps/angtype iso/gate/source/thyroid_Phantom/*
*gps/mintheta                 0. deg/gate/source/thyroid_Phantom/*
*gps/maxtheta                180. deg/gate/source/thyroid_Phantom/*
*gps/minphi                    0. deg/gate/source/thyroid_Phantom/*
*gps/maxphi                   360. deg/gate/source/thyroid_Phantom/*
*gps/confine                  NULL/gate/source/thyroid_Phantom/*
*setForcedUnstableFlag true/gate/source/thyroid_Phantom/*
*setForcedHalfLife    21636 s*
*/gate/source/list*

Other than substituting the above bold text, I found a snippet in the link
in the previous message stating that this */gate/source/thyroid_Phantom/*
*TranslateTheSourceAtThisIsoCen**ter *command must be used for .mhd files,
as opposed to

/gate/source/activityImage/setPosition

So with this I translate my source away from my collimator (centered at
0,0,0), by -2.0875 in the y-direction. Here my Qt output with a source
above my collimator / gamma camera setup:

[image: image.png]
And after processing the Singles output with python, I'm getting a clear
image of the thyroid:
[image: image.png]
Hope this comes in handy to someone!

-Chris


On Wed, Nov 20, 2019 at 8:50 AM Brosch, Julia <
Julia.Brosch at med.uni-muenchen.de> wrote:

> Hi Chris,
>
>
>
> when loading voxelized sources in GATE, they’re placed in the first
> quarter of the coordinate system. You can find details in the manual (
> https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html#voxelized-sources)
>  under “7.3.2 Position”. There is also an example provided, explaining how
> you need to shift your voxelized source accordingly.
>
>
>
> Try the command below instead of “/gate/source/thyroid_Phantom/gps/centre
> 0. 35. 0. Mm“ and adjust the shift „XX“ according to half of your image
> size. This command line is also in your example on page 146 of the v8.0
> manual version.
>
> /gate/source/ thyroid_Phantom /setPosition –XX –XX –XX mm
>
>
>
> I hope this helps you to place your source in the right position.
>
>
>
> Best,
>
> Julia
>
> *Von:* Gate-users <gate-users-bounces at lists.opengatecollaboration.org> *Im
> Auftrag von *Christopher Watanabe
> *Gesendet:* Dienstag, 19. November 2019 22:53
> *An:* gate-users at lists.opengatecollaboration.org
> *Betreff:* [Gate-users] Voxelized Source Problem
>
>
>
> Hi all,
>
> I'm facing problems importing a voxelized source into my simulation. My
> code below is very close to the code in the Gate Users' Manual V8.0, page
> 146.
>
> # Inserting Voxelized Source
> /gate/source/addSource                       thyroid_Phantom voxel
> /gate/source/thyroid_Phantom/reader/insert     image
> /gate/source/thyroid_Phantom/imageReader/translator/insert     linear
> /gate/source/thyroid_Phantom/imageReader/linearTranslator/setScale      2
> Bq
> /gate/source/thyroid_Phantom/imageReader/readFile
> ./data/thyroidPhantom/metaimage2.mhd
> /gate/source/thyroid_Phantom/imageReader/verbose 1
>
> /gate/source/thyroid_Phantom/gps/centre 0. 35. 0. mm
>
> /gate/source/voxel/gps/particle gamma
> /gate/source/voxel/gps/energytype Mono
> /gate/source/voxel/gps/monoenergy 140.5 keV
> /gate/source/voxel/gps/angtype iso
> /gate/source/voxel/gps/mintheta                 0. deg
> /gate/source/voxel/gps/maxtheta 90. deg
> /gate/source/voxel/gps/minphi                0. deg
> /gate/source/voxel/gps/maxphi                360. deg
> /gate/source/voxel/gps/confine NULL
> /gate/source/voxel/setForcedUnstableFlag true
> /gate/source/voxel/setForcedHalfLife    21636 s
>
> Where metaimage2.mhd is a binary mask of a thyroid scan. (0 background, 1
> thyroid).
>
> Despite this, I'm getting very strange visualization results from the
> simulation:
>
> [image: image.png]
>
> Strangely, the source doesn't move when I change the
> */gate/source/thyroid_Phantom/gps/centre* coordinates. I'm a bit at a
> loss of how to solve this problem.
>
> Has anyone had similar experiences with this? Is it a GATE issue, or is
> this more likely something that would originate from a faulty .mhd file
> formatting?
>
> Thank you!
>
> Chris
>
>
>
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