[Gate-users] brain phantom
Emilie Gaudin
Emilie.Odette.Gaudin at USherbrooke.ca
Wed Sep 18 16:31:16 CEST 2019
I used the voxelized source method.
Zubal and BigBrain images are segmented in different regions and each have an assigned voxel number.
For example (random values here):
0 is air
1 is the grey matter
2 is the withe matter
3 is the external cortex
4 is the cerebellum etc ...
You can use a real FDG image to evaluate the average activity in each segment and used it to create your activity range for your simulation (see the user guide wikipedia to help you with this).
Emilie
________________________________
De : Gate-users <gate-users-bounces at lists.opengatecollaboration.org> de la part de gate-users-request at lists.opengatecollaboration.org <gate-users-request at lists.opengatecollaboration.org>
Envoyé : 18 septembre 2019 03:58
À : gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Objet : Gate-users Digest, Vol 160, Issue 19
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Today's Topics:
1. Re: brain phantom (Emilie Gaudin)
2. Re: brain phantom (Svetlana Shasharina)
3. Re: brain phantom (Svetlana Shasharina)
4. Announcing RSim Application (Svetlana G. Shasharina)
5. IAEA phase space source
(MURPHY, James (ROYAL CORNWALL HOSPITALS NHS TRUST))
6. Re: max number of particles problem (Dimitrios Thanasas)
----------------------------------------------------------------------
Message: 1
Date: Tue, 17 Sep 2019 14:46:49 +0000
From: Emilie Gaudin <Emilie.Odette.Gaudin at USherbrooke.ca>
To: "gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] brain phantom
Message-ID:
<YQXPR0101MB1750B884F526F772BA6704E4AB8F0 at YQXPR0101MB1750.CANPRD01.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="iso-8859-1"
You can find the Zubal phantom (MRI based 1.5 mm) here: http://noodle.med.yale.edu/zubal/data.htm
and the BigBrain phantom (histology-based 400um) here: https://pet-mr.github.io/brain_phantom/
Images are already segmented, you only have to create the activity and attenuation range dat file.
Be sure to convert the images in .i33 with the appropriate header .h33
Emilie
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Message: 2
Date: Tue, 17 Sep 2019 08:53:31 -0600
From: Svetlana Shasharina <sveta at txcorp.com>
To: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] brain phantom
Message-ID: <482f55f8-3e4c-5b6b-9708-add924c268b6 at txcorp.com>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"
Thank you, Emilie!
Svetlana
On 9/17/19 8:46 AM, Emilie Gaudin wrote:
> You can find the Zubal phantom (MRI based 1.5 mm) here:
> http://noodle.med.yale.edu/zubal/data.htm
> and the BigBrain phantom (histology-based 400um) here:
> https://pet-mr.github.io/brain_phantom/
>
> Images are already segmented, you only have to create the activity and
> attenuation range dat file.
> Be sure to convert the images in .i33 with the appropriate header .h33
>
> Emilie
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
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Message: 3
Date: Tue, 17 Sep 2019 09:09:19 -0600
From: Svetlana Shasharina <sveta at txcorp.com>
To: Josh Knowland <jknowland at lucernodynamics.com>,
"gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>, Peter Neilson
<neilson at txcorp.com>
Subject: Re: [Gate-users] brain phantom
Message-ID: <a57371e2-27bc-10d1-bca0-448b5ea7eb6c at txcorp.com>
Content-Type: text/plain; charset=utf-8; format=flowed
Thank you, Josh! We will try Zubal first and see if we good STLs.
Have you used STLs objects as sources with activities assigned to them?
What is the method to close STLs? Some software that you developed?
Best,
Svetlana
On 9/17/19 8:36 AM, Josh Knowland wrote:
> Hi Svetlana - I could also use a brain phantom. If you send me the STL files, I can work to close the surfaces. I also work with STL files.
>
> -Josh
>
>
>
> -----Original Message-----
> From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> On Behalf Of Svetlana Shasharina
> Sent: Tuesday, September 17, 2019 10:35 AM
> To: gate-users at lists.opengatecollaboration.org; Peter Neilson <neilson at txcorp.com>
> Subject: [Gate-users] brain phantom
>
> Hi everybody,
>
> Does anybody have tested segmented brain STL or voxelized data to share or can point us to one? We worked with STL files created from
> http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 using splicer software, but we ended up with STL surfaces that were not closed.
>
> Thank you,
>
> Svetlana
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
------------------------------
Message: 4
Date: Tue, 17 Sep 2019 11:48:16 -0600
From: "Svetlana G. Shasharina" <sveta at txcorp.com>
To: "gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] Announcing RSim Application
Message-ID: <1aefe60e-1ee6-7d14-bd80-dda39a7037f6 at txcorp.com>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear GATE community,
Tech-X is developing RSim: a cross-platform GUI facilitating running
radiation transport simulations. It allows setting up simulations of GRAS:
http://space-env.esa.int/index.php/geant4-radiation-analysis-for-space.html.
RSim does not come with GRAS, though, and you can get it by registering
at https://essr.esa.int/register.
GRAS itself might not be interest for medical applications, but RSim
offers geometry creation and transformation functions which can be of
interest: creation of STLs from primitives and CAD (in STEP format).
You also can generate tetrahedral mesh in Tetgen format. When playing
with the tet meshes, be aware that we use Netgen under the hood and one
needs to play with the parameters before the tet mesh generation is
successful.
Anyway, you are welcome to download RSim by filling out the form at
https://www.txcorp.com/rsim.
Best regards,
Svetlana
--
Svetlana Shasharina | sveta at txcorp.com
Vice-President of Computational Infrastructure | Tech-X Corporation
------------------------------
Message: 5
Date: Tue, 17 Sep 2019 22:01:02 +0000
From: "MURPHY, James (ROYAL CORNWALL HOSPITALS NHS TRUST)"
<james.murphy18 at nhs.net>
To: "gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] IAEA phase space source
Message-ID: <1568757663275.48859 at nhs.net>
Content-Type: text/plain; charset="iso-8859-1"
Hi
Is there a way to filter the particles from the IAEA phase space source, I just want the photons.
Thanks
James
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Message: 6
Date: Wed, 18 Sep 2019 11:12:36 +0300
From: "Dimitrios Thanasas" <dthanas at uoa.gr>
To: "Emilie Gaudin" <Emilie.Odette.Gaudin at USherbrooke.ca>
Cc: "gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] max number of particles problem
Message-ID:
<1fb9d8b8622221ddab812db44d12abc7.squirrel at webmail01.uoa.gr>
Content-Type: text/plain;charset=utf-8
Hi Emilie,
Thanks for your answer. I tried it and it didn't work.
I don't produce output files with singles (or hits) events.
I use only dose actors, so the output file contains dose or/and energy
deposited.
It seems it doesn't work with Actors.
I found a solution using activity and time to produce more than 2 billion
particles.
Thanks again,
Dimitris
> Hi Dimitri,
>
>
> To bypass the 2GB file size the command line is:
>
> /gate/output/ascii/setOutFileSizeLimit 0
>
>
> The zero at the end of the line implies an unlimited file size (validated
> with GATE v7.0/7.2/8.0/8.1). This restriction is true for ascii/binary
> output.
>
> If you don't need the ascii, you can use the root output. It provides all
> the information needed with a significantly lower file size than asciis.
>
>
> Emilie
>
>
> ________________________________
> De : Gate-users <gate-users-bounces at lists.opengatecollaboration.org> de la
> part de gate-users-request at lists.opengatecollaboration.org
> <gate-users-request at lists.opengatecollaboration.org>
> Envoyé : 13 septembre 2019 08:56
> À : gate-users at lists.opengatecollaboration.org
> <gate-users at lists.opengatecollaboration.org>
> Objet : Gate-users Digest, Vol 160, Issue 13
>
> Send Gate-users mailing list submissions to
> gate-users at lists.opengatecollaboration.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> or, via email, send a message with subject or body 'help' to
> gate-users-request at lists.opengatecollaboration.org
>
> You can reach the person managing the list at
> gate-users-owner at lists.opengatecollaboration.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Gate-users digest..."
>
>
> Today's Topics:
>
> 1. max number of particles problem (Dimitrios Thanasas)
> 2. Change orientation of cone volume (Christopher Watanabe)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 13 Sep 2019 14:49:09 +0300
> From: "Dimitrios Thanasas" <dthanas at uoa.gr>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] max number of particles problem
> Message-ID:
> <0688552fc89d96ae9de4a83d7fc9a96d.squirrel at webmail01.uoa.gr>
> Content-Type: text/plain;charset=utf-8
>
> Hi everyone,
>
> I noticed that the simulation doesn't proceed when I use more than 2E+9
> particles. Does anyone know how I can use more than 2 billion particles?
> I found the command "/gate/output/ascii(binary)/setOutFileSizeLimit" at
> the User's Guide but it doesn't work.
> Moreover I don't want ascii files as I use dose actors for dose
> calculations and I want many particles to reduce the dose uncertainty.
>
> Thanks in advance,
> Dimitris Thanasas
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 13 Sep 2019 15:10:38 +0200
> From: Christopher Watanabe <chris.r.watanabe at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Change orientation of cone volume
> Message-ID:
> <CAKsu_TbQWJkc-Mu05088LH8K=OTTjJZE0oOyAKwEOgT_VUVt2Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi everyone,
>
> I'm trying to create a pinhole collimater. So far, I have everything set
> up
> well, but the orientation is wrong with the preexisting orientation of the
> camera. (i.e. the primary axis of the pinhole should be the normal of the
> pixel grid)
>
> The code I have now is:
>
> ## Volume at the front of the spect device for the collimator
>
> /gate/front/daughters/name collimator
> /gate/front/daughters/insert box
> /gate/collimator/geometry/setXLength 44. mm
> /gate/collimator/geometry/setYLength 11.14 mm
> /gate/collimator/geometry/setZLength 44. mm
> /gate/collimator/placement/setTranslation 0. -0.2 0. mm
> /gate/collimator/setMaterial Air
>
> # Square of tungsten with correct thickness at the wider base (crystal
> side)
> /gate/collimator/daughters/name base
> /gate/collimator/daughters/insert box
> /gate/base/geometry/setXLength 44. mm
> /gate/base/geometry/setYLength 1 mm
> /gate/base/geometry/setZLength 44. mm
> /gate/base/placement/setTranslation 0. -0.2 0. mm
> /gate/base/setMaterial Tungsten
>
> # Cone of tungsten for collimation
> /gate/collimator/daughters/name Tcone
> /gate/collimator/daughters/insert cone
> /gate/Tcone/geometry/setRmin1 0 mm
> /gate/Tcone/geometry/setRmax1 3 mm
> /gate/Tcone/geometry/setRmin2 0 mm
> /gate/Tcone/geometry/setRmax2 25 mm
> /gate/Tcone/geometry/setHeight 11.14 mm
> /gate/Tcone/placement/setTranslation 0. -0.2 0. mm
> /gate/Tcone/setMaterial Tungsten
>
> # Cone of Air within the cone of tungsten
> /gate/Tcone/daughters/name hole2
> /gate/Tcone/daughters/insert cone
> /gate/hole2/geometry/setRmin1 0 mm
> /gate/hole2/geometry/setRmax1 2 mm
> /gate/hole2/geometry/setRmin2 0 mm
> /gate/hole2/geometry/setRmax2 24 mm
> /gate/hole2/geometry/setHeight 11.14 mm
> /gate/hole2/placement/setTranslation 0. -0.2 0. mm
>
> So, basically, the hollow tungsten cone should be within the air volume
> allocate for the collimator. The primary axis of the cone is along the z
> direction though, so I get the following visualization:
>
> [image: image.png]
> As you can see, the solid red cone (pinhole) is oriented along the z-axis,
> whereas the rest of the SPECT device is oriented along the y axis...
>
> Things I've tried:
> /gate/Tcone/placement/alignToY - This command just centers it along the y
> axis. Doesn't change the primary axis.
> /gate/Tcone/placement/setRotationAxis +
> /gate/Tcone/placement/setRotationAngle - Also doesn't yield any helpful
> changes.
>
> I'd appreciate any help!
>
> Cheers!
>
> Chris
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