[Gate-users] Easy Gate Installation

[maxime]

Dear all,

I saw the problem you mention in 1. quite some times and even with GATE examples.
It happens when you execute visualisation commands early in your main.mac
If you move your /control/execute visu.mac right before the application start command it will run fine.
I don’t know what causes this error. I reported an issue on the GitHub:
https://github.com/OpenGATE/Gate/issues/203 <https://github.com/OpenGATE/Gate/issues/203>

Best regards,
  Maxime Chauvin

> On 24 Jan 2019, at 23:14, kirova at mskcc.org <kirova at MSKCC.ORG> wrote:
> 
> Hi Alexandre,
>  
> Thank you so much for the prompt response!
>  
> The .mac script runs well on a different installation.  It is just a simple geometry with three materials and a histogram defined source.
> So we don’t open any files. The error seems to be that during the initialization
> GateImageT.icc (l.75): tries to open a file different from 
> .vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm : 
>  
> “PreInit> /gate/run/initialize
> …
> [Core-0] Initialization of actors
> GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :
> .vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm”
>  
> The source-gatev8.1 alias could not run for us after running the installation script. 
> So we just source gate_enc.sh and that allows us to run Gate.
> That is how we run it on another machine without errors but also without visualization.
>  But maybe source-gatev8.1 does more than gate_env.sh and that may fix the above problem ?
> Where is it? I could not find it.
>  
> Daniel is an excellent programmer who will be learning GATE and I advised him to request a collaborative account.
>  
> Thanks again,
> Assen
>  
>  
> From: Alexandre CARRÉ [mailto:xela.errac at gmail.com <mailto:xela.errac at gmail.com>] 
> Sent: Thursday, January 24, 2019 4:26 PM
> To: Kirov, Assen/Medical Physics <kirova at MSKCC.ORG <mailto:kirova at MSKCC.ORG>>
> Cc: gate-users <gate-users at lists.opengatecollaboration.org <mailto:gate-users at lists.opengatecollaboration.org>>; Lafontaine, Daniel/Medical Physics <lafontad at mskcc.org <mailto:lafontad at mskcc.org>>
> Subject: [EXTERNAL] Re: Re: [Gate-users] Easy Gate Installation
>  
> Hello assen,
>  
> 1) For the error, I can't tell you where it came from without seeing the script that was run.
>  
> 2) source-gatev8.1 is an alias for sourcing environment variables. So you need to execute 'source-gatev8.1' and then 'Gate'.
>  
> Alexandre CARRE
>  
>  
> Le jeu. 24 janv. 2019 à 21:07, <kirova at mskcc.org <mailto:kirova at mskcc.org>> a écrit :
> Hi  Alexandre and all,
>  
> We just used the script and it is really of great help – thank you very much!
> I had not installed it for a very long time.
>  
> Just a couple of comments: 
> 1)When trying it we get this error:
>  
> PreInit> /gate/run/initialize
> [Core-0] Initialization of geometry
> [Core-0] Initialization of physics
> [Physic-0] WARNING: manual physic lists are being deprecated.
> Please, use physic list builder mechanism instead. Related documentation can be found at:
> http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics <http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics>
> [Core-0] Initialization of actors
> GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :
> .vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm
>  
> Do you have any clues what may be wrong?
>  
> 2)On the github explanation before running Gate,
> I guess you mean to source gate_env.sh
> you have something else there.
>  
> I am copying to this message our new colleague Daniel Lafontaine,
> who will join the collaboration soon.
>  
> Thanks again,
> Assen
>  
> --
> Assen S. Kirov, Ph.D., DABR
> Associate Attending Physicist
> Department of Medical Physics
> room S-1119G
> tel: (212) 639-7126
>  
>  
>  
>  
> From: Gate-users [mailto:gate-users-bounces at lists.opengatecollaboration.org <mailto:gate-users-bounces at lists.opengatecollaboration.org>] On Behalf Of Alexandre CARRÉ
> Sent: Monday, November 26, 2018 5:50 AM
> To: joao.marcos at coimbra.lip.pt <mailto:joao.marcos at coimbra.lip.pt>; gate-users <gate-users at lists.opengatecollaboration.org <mailto:gate-users at lists.opengatecollaboration.org>>
> Subject: [EXTERNAL] Re: [Gate-users] Easy Gate Installation
>  
> Great to hear that ! I'm glad that you like it.
>  
> Best regards,
>  
> Have a nice week.
>  
> Le lun. 26 nov. 2018 à 11:17, João Marcos <joao.marcos at coimbra.lip.pt <mailto:joao.marcos at coimbra.lip.pt>> a écrit :
> Alexandre,
> 
> 
> I will definitely use your script. Thank you very much for make it
> available for all.
> I have just installed the docker version of Gate.
> 
> Have a nice week.
> Regards,
> João Marcos
> 
> 
> On Sun, 25 Nov 2018 11:20:33 +0100, Alexandre CARRÉ
> <xela.errac at gmail.com <mailto:xela.errac at gmail.com>>
> wrote:
> > Hello GATE community,
> > 
> > I have developed a small script that allows you to install GATE in a
> simple
> > way. In addition, new users often have difficulty installing GATE, which
> > can help them.
> > I hope this tool will be useful.
> > 
> > It is available at the following address:
> > https://github.com/Alxaline/Easy-GATE-Installation <https://github.com/Alxaline/Easy-GATE-Installation>
> > 
> > Best regards,
> ᐧ
> 
> 
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