[Gate-users] GATE-user newsletter (January, 2013)

[GATE]

Dear GATE-users,
We are happy to announce the release of the first GATE-user newsletter of  
this year. We take this opportunity to wish you all the best for 2013.
Albertine Dubois, for the OpenGATE collaboration

Can't view this email properly? Click *here*  
http://www.opengatecollaboration.org/Newsletter-gate-users-jan2013 for the  
online version

  GATE
    Simulations of Preclinical and Clinical Scans in Emission Tomography,  
Transmission Tomography and Radiation Therapy
    *opengatecollaboration.org* http://www.opengatecollaboration.org

*GATE-user newsletter*
January, 2013 / issue 2
LATEST NEWS
*BEST WISHES FOR 2013!*
On behalf of the entire OpenGATE collaboration, we wish you a happy, healthy  
and successful new year.

*** The current public release of GATE is *V6.2*  
http://www.opengatecollaboration.org/GATE620release, including the new  
features previously listed *here*  
http://www.opengatecollaboration.org/Newsletter-gate-users-sept2012 and in  
which a number of bugs have been corrected (regular navigator and ion sources  
issues, especially). It has been released on September, 4th.
*** The next public release after GATE V6.2 will be GATE V7 and planned to be  
available during spring 2013.
- V7.0 will contain dedicated tools to complete fluorescence and  
bioluminescence optical imaging simulations.
- V7.0 will also include the first GPU modules (additional ones will be  
released later). This release will be offered to the users as a single  
package with the choice between CPU and GPU implementation of GATE processes.
*** A QSPECT toolkit for SPECT image reconstruction has been developed by  
members of the Department of Medical Instruments Technology in Athens and can  
be downloaded at *www.teiath.gr/stef/tio/ni/EnglishVersion/nuc_engl.html*  
http://www.teiath.gr/stef/tio/ni/EnglishVersion/nuc_engl.html (download  
section). QSPECT runs on linux and can import directly ROOT files from GATE  
simulations.
QUIZZ OF THE LAST NEWSLETTER

/A was the GATE-simulated image while B was the patient image. Please see  
*Stute et al, Phys Med Biol 2012*  
http://www.ncbi.nlm.nih.gov/pubmed/21934192/
TRAINING SESSIONS
The next GATE training session will take place February 12-13-14, 2013, in  
Saclay, near Paris, France. Instructors will be Irène Buvat, Albertine  
Dubois, Sebastien Jan and Simon Stute.
Two days will be devoted to using and running GATE (setting up and launching  
simulations, source description, analytical phantoms, voxelized phantoms,  
data output, digitizer and dead time modeling, modeling radiotherapy  
experiments) and the remaining day will be dedicated to building a simulation  
with Geant4 and to C++ developments in GATE. Training includes a lot of  
hands-on to get familiar with using GATE.
Registration fees are 930 € for three days including lunch and coffee  
breaks, part of the transportation and training material. The maximum number  
of attendees is almost reached, so if you are interested in attending this  
training session, please quickly visit this *page*  
http://www.opengatecollaboration.org/GATEtraining2013 for all practical  
details, registration form and detailed program.


SPECIAL FOCUS ON GATELAB
GateLab is a web browser application to easily launch Gate simulations on a  
large computing infrastructure. GATE simulations are executed with tens or  
hundreds of computers in parallel on the European Grid Infrastructure (*EGI*  
http://www.egi.eu).

GateLab's main features are:
*** One click submission from a web browser: upload your main macro file, the  
system will detect and upload all additional files necessary for your  
simulations.
*** Simulation monitoring.
*** Automatic results merging: once the simulation is completed, results are  
ready for download on your workstation.

GateLab system started in 2008. After a test version released in 2011, a beta  
version of GateLab has been made available to the users since February 2012.  
Since then, 187 users registered, launching about 200 simulations per month.  
The global average speedup of simulations is around 50 (taking queing and  
merging into account) but it is not rare to reach speedup greater than 200.  
The record is about 350 times faster.
Because the GateLab system is quite new, there are still some limitations.  
For instance, the fastest mode (dynamic mode) can only be used for radiation  
therapy applications. Static mode has to be used for PET/SPECT simulations.  
The main limitation concerns PET simulations having multiple runs that cannot  
yet be launched with GateLab. GateLab's team is working on it.

How to start and find more detailed information ?
Go to the following *page* http://vip.creatis.insa-lyon.fr and ask for an  
account. You can also find some information visiting  
*www.opengatecollaboration.org/GateLab*  
http://www.opengatecollaboration.org/GateLab.


RECENT GATE-RELATED PUBLICATIONS
*** Aguiar P, Iglesias A, Couce B, Lois C. A feasibility study on the use of  
arrays of discrete SiPMs for MR compatible LYSO readout using Monte Carlo  
simulation. Journal of Instrumentation. 7 (2012) P06002
*** Le Maitre A, Hatt M, Pradier O, Cheze-le Rest C, Visvikis D. Impact of  
the accuracy of automatic tumour functional volume delineation on  
radiotherapy treatment planning. Phys Med Biol. 57 (2012) 5381-97
*** Hatt M, Maitre AL, Wallach D, Fayad H, Visvikis D. Comparison of  
different methods of incorporating respiratory motion for lung cancer tumor  
volume delineation on PET images: a simulation study. Phys Med Biol. 57  
(2012) 7409-30
*** Fan Q, Nanduri A, Mazin S, Zhu L. Emission guided radiation therapy for  
lung and prostate cancers: a feasibility study on a digital patient. Med  
Phys. 39 (2012) 7140-52
*** Fuchs H, Strobele J, Schreiner T, Hirtl A, Georg D. A pencil beam  
algorithm for helium ion beam therapy. Med Phys. 39 (2012) 6726-37

If you wish to have your GATE-related papers listed here and/or on the GATE  
website, please send the complete reference to *us*  
mailto:dubois at imnc.in2p3.fr.
Copyright (c) the OpenGATE collaboration

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