[Gate-users] LUT Davis model -users Digest, Vol 159, Issue 16

Tue Aug 13 12:40:05 CEST 2019

Dear Simon,

Find the LUTs to download here: https://geant4.web.cern.ch/support/download (G4RealSurface2.1.1)
The “Enabling_LUT_Davis_Model” option was meant to bridge the time period between the geant4 and Gate releases when the model was first released in 2018. You should not have to go through that process anymore.

Just follow the regular installation procedure of geant4 and Gate and enable the LUTDavis options.
In ccmake for geant4 use flag GEANT4_INSTALL_DATA to download the data from the link above.
In ccmake for Gate use flag GATE_USE_DAVIS.

Let us know if it worked!
Best wishes,
Mariele

On 13 Aug 2019, at 12:00, gate-users-request at lists.opengatecollaboration.org<mailto:gate-users-request at lists.opengatecollaboration.org> wrote:

Send Gate-users mailing list submissions to
gate-users at lists.opengatecollaboration.org<mailto: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. Re: VGate (Howard)
  2. Re: Enabling LUT Davis model (David Boersma)

----------------------------------------------------------------------

Message: 1
Date: Mon, 12 Aug 2019 14:41:59 -0400
From: Howard <lomahu at gmail.com>
To: tmerlin <Thibaut.Merlin at univ-brest.fr>
Cc: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] VGate
Message-ID:
<CAKr9h5X4ZAhA9q-sfn=v7scDeohdZQKY5M5bO6GuxKSho+vFTA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Thibaut,

The replacement of those lines, ie, replacing interfile with image and
interfileReader with imageReader, did the trick. It is working now. Thanks!

Howard

On Mon, Aug 12, 2019 at 2:28 PM tmerlin <Thibaut.Merlin at univ-brest.fr>
wrote:

Hi Howard,

In the macros/VoxelizedSource.mac file, try to replace the following lines:

*/gate/source/voxel_brain/reader/insert interfile*
*/gate/source/voxel_brain/interfileReader/translator/insert range*
*/gate/source/voxel_brain/interfileReader/rangeTranslator/readTable
./phantom/activity_range.dat*
*/gate/source/voxel_brain/interfileReader/rangeTranslator/describe 1*
*/gate/source/voxel_brain/interfileReader/readFile
./phantom/brain_phantom.h33*

by:

*/gate/source/voxel_brain/reader/insert image*
*/gate/source/voxel_brain/imageReader/translator/insert range*
*/gate/source/voxel_brain/imageReader/rangeTranslator/readTable
./phantom/activity_range.dat*
*/gate/source/voxel_brain/imageReader/rangeTranslator/describe 1*
*/gate/source/voxel_brain/imageReader/readFile ./phantom/brain_phantom.h33*

Hope this works for you

Cheers,

Thibaut Merlin

On 12/08/2019 19:52, Howard wrote:

Hi David,

Thank you for taking the time to reply to my question. I am using Gate
v8.2 and was trying to run the example provided in the following training
session:

http://www.opengatecollaboration.org/Materials2015/PracticalExercises2015/VoxelizedSources&Phantoms

The error was similar to the one reported by PAT back in August 2018:

GateSourceVoxelInterfileReader.cc (l.25): GateSourceVoxelInterfileReader
is obsolete, use GateSourceVoxelImageReader instead!

I wonder whether there is a workaround to this error. Many thanks!

Howard

On Mon, Aug 12, 2019 at 4:51 AM David Boersma <david.boersma at acmit.at>
wrote:

Hi Howard and PAT,

Which version of VGate are you using? Could you try the latest release
(8.2, released in February)?

And are you referring to the "shared disk" issue or the  "interfile"
issue?

If the latter: I searched the current version of GateContrib and I do not
find any references to "GateSourceVoxelInterfileReader". It's possible
that this has been fixed in the meantime. So then the solution would be to
run "git pull" in your GateContrib clone and check what happened to the
example that you are referring to (I'm not sure which example that is).
It's possible that this particular example has actually been removed in the
meantime.

I hope that this helps a bit. If it doesn't, then I hope that an imaging
expert (which I am not) will come back from vacation soon and give a better
answer your question. 😊

Good luck,

David Boersma
------------------------------
*Von:* Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
im Auftrag von Howard <lomahu at gmail.com>
*Gesendet:* Freitag, 9. August 2019 22:50:10
*An:* gate-users at lists.opengatecollaboration.org
*Betreff:* Re: [Gate-users] VGate

Dear Gate-users,
Does anyone happen to know the workaround the problem as PAT reported
back in August, 2018? Thanks very much.
Howard [Gate-users] VGate *P. T.* ptpphysics at gmail.com
<gate-users%40lists.opengatecollaboration.org?Subject=Re%3A%20%5BGate-users%5D%20VGate&In-Reply-To=%3CCAJ9ZRTLFukiRprD_UOQAjEcxVo_POgumWpUGzTA%3DrxDU1eBkMg%40mail.gmail.com%3E>
*Sat Aug 25 12:14:02 CEST 2018*

  - Previous message: [Gate-users] Physics list usage for medical
  imaging simulations
  <http://lists.opengatecollaboration.org/pipermail/gate-users/2018-August/010378.html>
  - Next message: [Gate-users] Seeking Experienced Optical Tracking
  Users for Help and Advice
  <http://lists.opengatecollaboration.org/pipermail/gate-users/2018-August/010380.html>
  - *Messages sorted by:* [ date ]
  <http://lists.opengatecollaboration.org/pipermail/gate-users/2018-August/date.html#10379>
   [ thread ]
  <http://lists.opengatecollaboration.org/pipermail/gate-users/2018-August/thread.html#10379>
   [ subject ]
  <http://lists.opengatecollaboration.org/pipermail/gate-users/2018-August/subject.html#10379>
   [ author ]
  <http://lists.opengatecollaboration.org/pipermail/gate-users/2018-August/author.html#10379>

------------------------------

Dear Gate expert,

Shared folder not working in new vgate. Furthermore, Example related
to Voxelized Phantom _Source don't execute correctly and show error:

GateSourceVoxelInterfileReader.cc (l.25):
GateSourceVoxelInterfileReader is obsolete, use
GateSourceVoxelImageReader instead!

Regards,
PAT

_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

_______________________________________________
Gate-users mailing listGate-users at lists.opengatecollaboration.orghttp://lists.opengatecollaboration.org/mailman/listinfo/gate-users

--
Thibaut MERLIN -- PhD

Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90

_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20190812/143f0f57/attachment-0001.html>

------------------------------

Message: 2
Date: Tue, 13 Aug 2019 09:17:14 +0000
From: David Boersma <david.boersma at acmit.at>
To: simon templar <treean01 at hotmail.com>,
"gate-users at lists.opengatecollaboration.org"
<gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Enabling LUT Davis model
Message-ID: <a4cbd0fb3d39448c8aa2f8156a09b17b at acmit.at>
Content-Type: text/plain; charset="big5"

Dear Simon,

It looks like those tables are stored on the "midas3" servers of KitWare, where we used to store also other Gate-related data files. Unfortunately KitWare decided to discontinue that service in summer 2018. Since this is technically kind of a bug, requiring action by developers to fix it, I created a GitHub issue for it: https://github.com/OpenGATE/Gate/issues/256

Hopefully this gets resolved quickly. Sorry for the inconvenience!

/David

________________________________
Von: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> im Auftrag von simon templar <treean01 at hotmail.com>
Gesendet: Montag, 12. August 2019 17:38:18
An: gate-users at lists.opengatecollaboration.org
Betreff: [Gate-users] Enabling LUT Davis model

Dear Gate-users,
I want to enable the LUT davis model with GATE version 8.0. When I followed the installation guide of website Enabling_LUT_Davis_Model<http://wiki.opengatecollaboration.org/index.php/Enabling_LUT_Davis_Model> to manually modifying GEANT4. I found the web link LUTs<https://midas3.kitware.com/midas/download/item/321835/Davis_LUTs.tar.gz>  of step 2 was fail. Does anyone else know how to download the LUTs I need.

Simon Wang
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20190813/0500d95d/attachment-0001.html>

------------------------------

Subject: Digest Footer

_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

------------------------------

End of Gate-users Digest, Vol 159, Issue 16
*******************************************

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20190813/589c520a/attachment-0001.html>