[Gate-users] Gate-users Digest, Vol 98, Issue 18
jehangir khan
jehangir.kahn at gmail.com
Thu Jul 10 16:15:24 CEST 2014
> Dear Gate users!
>
> Can anybody share information or experience for vGate installation on
clusters.
> I have installed VGate successfully on My main cluster. My question is ,
do I need to install vGate On each clusters respectively? After that
install NFS , and MPI for sharing folder ?
> I shall appreciate for response or suggestion
> Best Regards
> Jehangir
On Thu, Jul 10, 2014 at 2:49 PM, <
gate-users-request at lists.opengatecollaboration.org> wrote:
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> Today's Topics:
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> 1. Re: Orientation of mhd file (Albert Hirtl)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 10 Jul 2014 15:37:26 +0200
> From: Albert Hirtl <albert.hirtl at meduniwien.ac.at>
> To: J?r?me Suhard <jerome at suhard.fr>
> Cc: gate-users <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Orientation of mhd file
> Message-ID: <53BE9716.7080306 at meduniwien.ac.at>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Hi,
>
> Ok thanks for your help and the clarification.
>
> By the way, is there a method to visualize voxelized sources which are
> read in from an interfile? At least I wasn't able to visualize it in
> order to check whether it is located where it should be.
>
> My workaround would be to read it in as phantom an check the position.
> However, in the manual it says, that I have to shift the source by half
> in -x and -y direction. Is there a better way to check the position?
>
> Cheers,
> Albert
>
> On 10/07/14 15:28, J?r?me Suhard wrote:
> > Hi,
> >
> > I can reproduce it.
> > Technically, my OpenGL custom commands are called one first time even
> > in Stored mode. At this moment, it seems that the rotation was not yet
> > applied.
> > But with X11 in Stored mode, there is no "refresh" of the graphical
> > scene thus leading to this artifact, you can remove it by forcing it
> with:
> > /vis/viewer/refresh
> >
> > Best regards,
> >
> >
> > 2014-07-10 9:25 GMT+02:00 Albert Hirtl <albert.hirtl at meduniwien.ac.at
> > <mailto:albert.hirtl at meduniwien.ac.at>>:
> >
> > Dear Simon,
> >
> > Thanks for the header. I thought it's best if I simply sent you
> > some screen shots from my system (attached). I hope the names make
> > clear what's in the image. Summarized one can say, that OGLIX does
> > what it should, OGLSX, however, at least on my system, does not
> > what I expect it to do.
> >
> > The command
> >
> > glxinfo | grep "OpenGL version"
> >
> > gives
> >
> > OpenGL version string: 2.1 Mesa 9.0-devel
> >
> > I am running Scientific Linux 6.0.
> >
> > Maybe everything is as it is expected to be? And simply I
> > misunderstand the properties of OGLSX?
> >
> > Cheers,
> > Albert
> >
> >
> > On 09/07/14 16:59, Simon Rit wrote:
> >> Thanks for sharing the data with us. I tested on my computer and
> >> I have the expected behavior, i.e.,
> >> - the image is upside down because Y goes from bottom to the top
> >> on Gate and it's the opposite in VV,
> >> - if I set
> >> /gate/patient/placement/setRotationAngle 180 deg
> >> then it is back to its normal position
> >> - same thing if I use the enclosed mhd but it is now upside down
> >> in VV
> >> - if I do the last two points together, it's back to the original
> >> position.
> >> Is this not what you observe?
> >> Simon
> >>
> >>
> >> On Wed, Jul 9, 2014 at 3:55 PM, Albert Hirtl
> >> <albert.hirtl at meduniwien.ac.at
> >> <mailto:albert.hirtl at meduniwien.ac.at>> wrote:
> >>
> >> Hi,
> >>
> >> Please find attached my very basic macros and the header of
> >> my image file that I used to play around with the .mhd
> >> feature (as tar archive). I can not send the raw data, since
> >> even if I gzip them they are larger than 11 MB and my mail is
> >> rejected. Do you have a mailbox which accepts more than 11 MB?
> >>
> >> Thanks again and cheers,
> >> Albert
> >>
> >>
> >>
> >>
> >> On 09/07/14 15:32, J?r?me Suhard wrote:
> >>> X stands for X11 (old static window)
> >>> Qt stands for ... Qt ( GUI with mouse support)
> >>>
> >>> S(tored) mode: you just see a box
> >>> I(mmediate) mode: you see your image with Gate7
> >>>
> >>> so OGLS or OGLI should not change orientation and/or
> rotation...
> >>>
> >>> If you have time to send me your CT/macro, I'm still
> >>> interested by them
> >>>
> >>>
> >>> 2014-07-09 15:24 GMT+02:00 Albert Hirtl
> >>> <albert.hirtl at meduniwien.ac.at
> >>> <mailto:albert.hirtl at meduniwien.ac.at>>:
> >>>
> >>> Hi,
> >>>
> >>> Thanks for the prompt answer, it was already enough to
> >>> solve the problem:
> >>>
> >>> I initially copied the following line from the
> >>>
> example_PHANTOM_SOURCE/Voxelized_Phantom_Source/mainMacro.mac
> >>>
> >>> /vis/open OGLSX
> >>>
> >>> Motivated by your answer I tried OGL*I*X and everything
> >>> is fine... Now all orientations are correct and
> >>> rotations work properly.
> >>>
> >>> So, could OGLSX be a typo in the example?
> >>>
> >>> Thanks a lot for you help!
> >>>
> >>> Cheers,
> >>> Albert (a bit embarrassed :-[ )
> >>>
> >>>
> >>>
> >>> On 09/07/14 15:09, J?r?me Suhard wrote:
> >>>> Hi,
> >>>>
> >>>> 2014-07-09 15:01 GMT+02:00 Albert Hirtl
> >>>> <albert.hirtl at meduniwien.ac.at
> >>>> <mailto:albert.hirtl at meduniwien.ac.at>>:
> >>>>
> >>>> If I display the CT using OGLSX it seems to be
> >>>> bottom up.
> >>>>
> >>>>
> >>>> You mean OGL*I*X, right ?
> >>>>
> >>>> /gate/patient/placement/setRotationAxis 0 0
> 1
> >>>> /gate/patient/placement/setRotationAngle
> >>>> XXXX deg
> >>>>
> >>>> it stays the same. In vv it was in the correct
> >>>> orientation. The box that is plotted around the CT
> >>>> seems to be rotating, however. Do I make anything
> >>>> wrong? Or is just the image that I see in OGLSX not
> >>>> rotating?
> >>>>
> >>>>
> >>>> can you give the most small macro with the CT showing
> >>>> this behaviour ?
> >>>>
> >>>> thanks
> >>>>
> >>>> --
> >>>> J?r?me Suhard
> >>>
> >>>
> >>> --
> >>> Medizinische Universit?t Wien
> >>> Universit?tsklinik f?r Radiologie und Nuklearmedizin
> >>> W?hringer G?rtel 18-20
> >>> 1090 Wien
> >>> Austria
> >>>
> >>> Tel.:+43 (0) 1 / 40400 55450
> <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
> >>>
> >>> Web:
> >>> http://www.meduniwien.ac.at/user/albert.hirtl
> >>> http://www.meduniwien.ac.at/moccamed/
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> J?r?me Suhard
> >>
> >>
> >> --
> >> Medizinische Universit?t Wien
> >> Universit?tsklinik f?r Radiologie und Nuklearmedizin
> >> W?hringer G?rtel 18-20
> >> 1090 Wien
> >> Austria
> >>
> >> Tel.:+43 (0) 1 / 40400 55450
> <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
> >>
> >> Web:
> >> http://www.meduniwien.ac.at/user/albert.hirtl
> >> http://www.meduniwien.ac.at/moccamed/
> >>
> >>
> >> _______________________________________________
> >> Gate-users mailing list
> >> Gate-users at lists.opengatecollaboration.org
> >> <mailto:Gate-users at lists.opengatecollaboration.org>
> >>
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >>
> >>
> >
> >
> > --
> > Medizinische Universit?t Wien
> > Universit?tsklinik f?r Radiologie und Nuklearmedizin
> > W?hringer G?rtel 18-20
> > 1090 Wien
> > Austria
> >
> > Tel.:+43 (0) 1 / 40400 55450
> <tel:%2B43%20%280%29%201%20%2F%2040400%2055450>
> >
> > Web:
> > http://www.meduniwien.ac.at/user/albert.hirtl
> > http://www.meduniwien.ac.at/moccamed/
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > <mailto:Gate-users at lists.opengatecollaboration.org>
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >
> >
> >
> >
> > --
> > J?r?me Suhard
>
>
> --
> Medizinische Universit?t Wien
> Universit?tsklinik f?r Radiologie und Nuklearmedizin
> W?hringer G?rtel 18-20
> 1090 Wien
> Austria
>
> Tel.: +43 (0) 1 / 40400 55450
>
> Web:
> http://www.meduniwien.ac.at/user/albert.hirtl
> http://www.meduniwien.ac.at/moccamed/
>
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