[Gate-users] Easy Gate Installation

Thu Jan 31 17:18:48 CET 2019

Hi Assen,

glad to see you here again!! Hope everything is fine for you and your
family.
I have the same error message:

*[Core-0] Initialization of actors*

*GateImageT.icc (l.75): Unknown image file extension. Supported extensions
are : *

*.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm*

I have no solution and I spent a lot of time to try to understand what
happens. Please find hereafter some elements but (again) no solution:

- This error only occurs with Gate8.1 (Geant4.10.4) (no error with
Gate8.0/G4.10.3.2)

- This error (seems to) occurs when an actor is defined. No error if the
command allownooutput is used.

- This error is not systematic and not reproducible. You have to run 10
times a macro to check if you have or not the  problem.

- I think but I am not quite sure that this error has absolutely no cause
in GateImageT.icc

- I use Gate8.0 now and I am waiting for Gate8.2  (some weeks) to check if
this error is still there

Sorry, but this message won't help you much.

Best regards

Luc SIMON

Le lun. 28 janv. 2019 à 20:06, <kirova at mskcc.org> a écrit :

> Hi Alexandre and Maxime,
>
>
>
> Thank you very much for responding.   Actually disabling vis also give the
> error.
>
> Dan will answer your questions in more details, but the Ubuntu version I
> think was the one required.
>
> There were some errors in mid installation, but it said successfully
> installed at the end  and both on the other an on this computer we have
> v8.1.
>
> Dan will check few more things and will come back to you.
>
>
>
> Assen
>
>
>
>
>
>
>
> *From:* Alexandre CARRÉ [mailto:xela.errac at gmail.com]
> *Sent:* Sunday, January 27, 2019 12:25 PM
> *To:* Kirov, Assen/Medical Physics <kirova at MSKCC.ORG>; gate-users <
> gate-users at lists.opengatecollaboration.org>; Lafontaine, Daniel/Medical
> Physics <lafontad at mskcc.org>
> *Subject:* [EXTERNAL] Re: Re: [Gate-users] Easy Gate Installation
>
>
>
> Hello Assen,
>
>
>
> To better understand the problem :
>
> What is your Linux distribution ?
>
> Did you get any error during the installation ?
>
> When you have Gate is it version 8.1 or a previous installed version?
>
>
>
> Best regards,
>
>
>
> Alexandre
>
>
>
> Le jeu. 24 janv. 2019 à 23:14, <kirova at mskcc.org> a écrit :
>
> Hi Alexandre,
>
>
>
> Thank you so much for the prompt response!
>
>
>
>    1. 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”
>
>
>
>    1. 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]
> *Sent:* Thursday, January 24, 2019 4:26 PM
> *To:* Kirov, Assen/Medical Physics <kirova at MSKCC.ORG>
> *Cc:* gate-users <gate-users at lists.opengatecollaboration.org>;
> Lafontaine, Daniel/Medical Physics <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> 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
>
> [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] *On Behalf Of *Alexandre
> CARRÉ
> *Sent:* Monday, November 26, 2018 5:50 AM
> *To:* joao.marcos at coimbra.lip.pt; gate-users <
> 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> 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>
> 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
> >
> > Best regards,
>
> ᐧ
>
>
>
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>
>
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> Please note that this e-mail and any files transmitted from
> Memorial Sloan Kettering Cancer Center may be privileged, confidential,
> and protected from disclosure under applicable law. If the reader of
> this message is not the intended recipient, or an employee or agent
> responsible for delivering this message to the intended recipient,
> you are hereby notified that any reading, dissemination, distribution,
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-- 
___________________

SIMON Luc, Physicien Médical, PhD
Département d'Ingénierie et de Physique Médicale - IUCT-Oncopole -
Toulouse, FRANCE
INSERM UMR 1037 (CRCT) - Equipe 15 - Toulouse, FRANCE
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