[Gate-users] Gate-users Digest, Vol 92, Issue 35

Fri Jan 31 13:42:25 CET 2014

Many thanks for the information.

Mike

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Subject: Gate-users Digest, Vol 92, Issue 35

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Today's Topics:

  1. Re: Edep image output (thibaultmauxion)
  2. Define scanning geometry (Stephen Yip)
  3. Re: Define scanning geometry (Marc Chamberland)

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Message: 1
Date: Mon, 27 Jan 2014 11:31:29 -0500
From: thibaultmauxion <thibault.mauxion at gmail.com>
To: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Edep image output
Message-ID: <DB901663-D016-4803-970C-DE9C803D12D5 at gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Mike, 

Just had a quick look but  seems you have a "geometry vs source" issue. 
The origin of the scale for the voxelized source is not set in the center of the geometry but at one corner (never remember which one). 
To match both scales, you need to shift your voxelized source by half of its total dimension using SetPosition) 

for more info, see http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6:Voxelized_Source_and_Phantom
under voxelized source section. 

I would also make sure the size of the voxels is consistent for the geometry and the voxelized source. 

Hope this helps 

Thibault 

Post-doctoral fellow
Division of Medical Imaging Physics 
Johns Hopkins Medical Institutions
JHOC 4260, 601 N. Caroline street, Baltimore, MD, 21287
Tel: +1 410 502 3772
Fax: +1 410 614 1060
http://www.hopkinsradiology.org/dmip/

On Jan 27, 2014, at 11:09 AM, Mike Tabriz <mtabriz at yahoo.com> wrote:

> Dear GATE users,
> In an attempt to simulate collection of dose in thyroid (target) from activity in lungs (source) I get the following images. Capture 4 shows a head slice from the Zubal phantom. Capture 5 shows the Edep image output file at the same exact slice. What is curious about this output image is that the head appears to be embedded in the lungs!
>  
> Any opinions as to the cause of this phenomenon is greatly appreciated.
>  
> With thanks in advance,
> Mike 
> <Capture4.PNG><Capture5.PNG>_______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

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Message: 2
Date: Mon, 27 Jan 2014 21:40:52 +0100
From: Stephen Yip <stephen.fyip1 at gmail.com>
To: gate-users <gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] Define scanning geometry
Message-ID:
    <CADfqr+far8m4CF9C8+P=a8Zm7x3u8E5EZ7uiQd8wJV6KGpoAAA at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

I am trying to create a sub-volume & insert material to it.

For example:

/gate/world/daughters/name cylindricalPET
/gate/world/daughters/insert cylinder
/gate/cylindricalPET/setMaterial Water

It complained that
/home/gate/Progs/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc
.....GateMaterialDatabase: could not find the definition for material
'Water' in Material files....

It then kicked me out of vGate and closed OGLSX

Does anyone know what I did wrong?

Thanks,
Stephen
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Message: 3
Date: Tue, 28 Jan 2014 00:25:34 +0000
From: Marc Chamberland <MarcChamberland at cmail.carleton.ca>
To: Stephen Yip <stephen.fyip1 at gmail.com>
Cc: Gate Users <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Define scanning geometry
Message-ID: <AA9940EF-6CD7-4F2F-8626-B620B2665F94 at cmail.carleton.ca>
Content-Type: text/plain; charset="iso-8859-1"

Hi Stephen,

I've had something like that happen to me before. In my case, the culprit was either the wrong line endings (for example, Unix vs Windows line endings) in the material file, or some other invisible characters that threw off Gate when reading the file.

I suggest you create a new blank text file and copy the material database to that new text file (all within vGate). Then use this new material file.

And if this does not work, then I do not know what's going on.

Good luck!
Marc

__________________________

Marc Chamberland, MSc
PhD candidate
Department of Physics
Carleton University
Ottawa (ON)

On Jan 27, 2014, at 15:40, Stephen Yip <stephen.fyip1 at gmail.com<mailto:stephen.fyip1 at gmail.com>> wrote:

Hi,

I am trying to create a sub-volume & insert material to it.

For example:

/gate/world/daughters/name cylindricalPET
/gate/world/daughters/insert cylinder
/gate/cylindricalPET/setMaterial Water

It complained that /home/gate/Progs/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc<http://gatematerialdatabase.cc/> .....GateMaterialDatabase: could not find the definition for material 'Water' in Material files....

It then kicked me out of vGate and closed OGLSX

Does anyone know what I did wrong?

Thanks,
Stephen

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