Hi d.m.
The performance setting is in the "view settings panel" - this is accessed
through the spanner button on the toolbar.
Cheers,
Paul
On 28 August 2017 at 10:31, d m <[log in to unmask]> wrote:
> Paul,
>
> I tried to locate the 'Performance' option in the view settings panel, but
> I could not find it. I've attached a picture.
>
> I'm running Ubuntu 14.04 and I have fsl installed via neurodebian. I
> downloaded FSLeyes from here:
>
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes
>
> Thanks.
>
> d.m.
> ------------------------------
> *From:* FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
> paul mccarthy <[log in to unmask]>
> *Sent:* Sunday, August 27, 2017 2:04:30 PM
>
> *To:* [log in to unmask]
> *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>
> Hi D.m.,
>
> (Thanks Kristian!)
>
> FSLeyes may have defaulted to running in a lower performance mode, where
> it pre-renders slices for all of your loaded images. You can check this via
> the 'Performance' option in the view settings panel (the spanner button).
>
> If it is set to 'Fastest', then FSLeyes will work pre-generate images in
> the background. If you get acceptable performance with either of the other
> two choices (Better or 'Best looking'), then you can configure FSLeyes to
> default to them via the '-p' command line flag ('-p 2' for better, or '-p
> 3' for best looking).
>
> Cheers,
>
> Paul
>
> On 25 August 2017 at 13:00, d m <[log in to unmask]> wrote:
>
>> Kristian.
>>
>>
>> Thank You!
>>
>>
>> That workaround helped a great deal. I followed the steps described in
>> the wiki, and it worked.
>>
>>
>> The OpenGL version string is now 2.1, and I no longer receive error
>> messages.
>>
>>
>> The only additional steps were to place that mesa directory in a selected
>> path,e.g.,/path/mesa-10.1.3/. Substitute that path for `pwd` in this
>> line:
>>
>>
>> export LD_LIBRARY_PATH=`pwd`/build/linux-x86_64-debug/gallium/targets/libgl-xlib/:${LD_LIBRARY_PATH}
>>
>> becomes
>>
>>
>> export LD_LIBRARY_PATH=/path/mesa-10.1.3/build/linux-x86_64-debug/g
>> allium/targets/libgl-xlib/:${LD_LIBRARY_PATH}
>>
>>
>> Added the above line with the modified path to my .bashrc file.
>>
>>
>> Works fine now each time I call fsleyes from the command line.
>>
>>
>> One thing I noticed is that fsleyes used about 23% CPU power even while
>> open, but idle. Is this normal?
>>
>>
>> Thanks again.
>>
>>
>> d.m.
>>
>>
>> ------------------------------
>> *From:* FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
>> Kristian Loewe <[log in to unmask]>
>> *Sent:* Wednesday, August 23, 2017 4:33:59 PM
>> *To:* [log in to unmask]
>> *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>>
>> Hi d.m. and Paul,
>>
>> I think, x2go only supports GLX 1.2.
>>
>> Have you tried this workaround:
>> http://wiki.x2go.org/doku.php/wiki:development:glx-xlib-workaround ?
>>
>> Cheers,
>>
>> Kristian
>>
>>
>> On 23.08.2017 11:23, paul mccarthy wrote:
>> > Hi d.m.,
>> >
>> > Currently the graphics hardware on your remote machines is not being
>> > used at all - GLX redirects all graphics calls to the local machine
>> that
>> > you connect from. If you want to use the graphics cards on your server,
>> > then the only way I am aware of is via VirtualGL.
>> >
>> > If you want to continue using x2go/freenx, then unfortunately I don't
>> > know of a workaround for the problem you are experiencing. I have not
>> > been able to reproduce it. Hopefully Kristian or somebody else may be
>> > able to give some advice.
>> >
>> > Cheers,
>> >
>> > Paul
>> >
>> > On 22 August 2017 at 19:18, d m <[log in to unmask]
>> > <mailto:[log in to unmask] <[log in to unmask]>>> wrote:
>> >
>> > Kristian and Paul, thank you for your feedback.
>> >
>> >
>> > Yes, we do connect remotely to our server using x2go/freenx.
>> >
>> >
>> > I tried clearing the LIBGL_ALWAYS_INDIRECT environment variable. It
>> > still did not work. I think the problem is that I have more than one
>> > graphics card on our machine. We have a Matrox VGA controller and
>> > two NVIDIA 3-D controllers installed on the machine.
>> >
>> >
>> > We have other servers with one card installed (the same VGA
>> > controller ), and fsleyes works fine.
>> >
>> >
>> > Somehow we are reduced to Opengl 1.2 and OpenGL renderer string:
>> > Mesa GLX Indirect with our hybrid graphic card setup. Is there a
>> > workaround or solution for this to get fsleyes running?
>> >
>> >
>> > Thanks.
>> >
>> >
>> > d.m.
>> >
>> > ------------------------------------------------------------
>> ------------
>> > *From:* FSL - FMRIB's Software Library <[log in to unmask]
>> > <mailto:[log in to unmask] <[log in to unmask]>>> on behalf of
>> Kristian Loewe
>> > <[log in to unmask] <mailto:[log in to unmask]
>> <[log in to unmask]>>>
>> > *Sent:* Tuesday, August 8, 2017 4:03:02 PM
>> > *To:* [log in to unmask] <mailto:[log in to unmask]
>> <[log in to unmask]>>
>> > *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>> > Hi,
>> >
>> > If indirect rendering is not possible, another option is to use
>> > VirtualGL. With VirtualGL, you can use the server's GPU for
>> rendering
>> > and have the rendered results sent to your local or virtual X
>> server.
>> > Depending on the graphics setup, the network speed, and the data
>> size,
>> > this approach may also give you noticably better performance than
>> > indirect rendering.
>> >
>> > Cheers,
>> >
>> > Kristian
>> >
>> > On 08.08.2017 20:10, paul mccarthy wrote:
>> > > Hi d.m.,
>> > >
>> > > I guess you are running FSLeyes on a remote server, right? Try
>> clearing
>> > > the LIBGL_ALWAYS_INDIRECT environment variable, as documented
>> here:
>> > >
>> > > https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/userdoc/latest/
>> troubleshooting.html#opengl-1-4-or-newer-is-required-detected-version-1-2
>> > <https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/userdoc/latest
>> /troubleshooting.html#opengl-1-4-or-newer-is-required-
>> detected-version-1-2>
>> > >
>> > > Unfortunately if this doesn't work, I have not yet figured out a
>> > > solution for this problem.
>> > >
>> > > Cheers,
>> > >
>> > > Paul
>> > >
>> > > On 8 August 2017 at 17:45, d m <[log in to unmask] <
>> mailto:[log in to unmask] <[log in to unmask]>>
>> > > <mailto:[log in to unmask] <[log in to unmask]>>> wrote:
>> > >
>> > > Michael,
>> > >
>> > >
>> > > Thanks for the suggestion. That worked, but now I get the
>> following
>> > > error message after typing "./fsleyes":
>> > >
>> > >
>> > > WARNING __init__.py 595: create - GLContext
>> > > callback function raised RuntimeError: OpenGL 1.4 or newer is
>> > > required (detected version: 1.2
>> > > Traceback (most recent call last):
>> > > File "fsleyes/gl/__init__.py", line 589, in create
>> > > File "fsleyes/main.py", line 377, in realCallback
>> > > File "fsleyes/gl/__init__.py", line 314, in bootstrap
>> > > RuntimeError: OpenGL 1.4 or newer is required (detected
>> version: 1.2
>> > >
>> > > Have you or anyone seen this message? If so, what was the
>> solution?
>> > >
>> > >
>> > > Thanks.
>> > >
>> > >
>> > > d.m.
>> > >
>> > > ------------------------------------------------------------
>> ------------
>> > > *From:* FSL - FMRIB's Software Library <[log in to unmask] <
>> mailto:[log in to unmask] <[log in to unmask]>>
>> > > <mailto:[log in to unmask] <[log in to unmask]>>> on behalf
>> of Michael Firbank
>> > > <[log in to unmask] <
>> mailto:[log in to unmask] <[log in to unmask]>>
>> > > <mailto:[log in to unmask]
>> > <mailto:[log in to unmask]
>> <[log in to unmask]>>>>
>> > > *Sent:* Friday, July 7, 2017 5:16:57 PM
>> > >
>> > > *To:* [log in to unmask] <mailto:[log in to unmask]
>> <[log in to unmask]>>
>> > <mailto:[log in to unmask] <[log in to unmask]>>
>> > > *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>> > >
>> > > Hello
>> > >
>> > >
>> > > You can unzip the folder wherever you like. Probably the
>> $FSLDIR/bin
>> > > is not the best place.
>> > >
>> > > In any case the fsleyes file needs to be in a directory on
>> your path.
>> > >
>> > > if you need to see what that is, type
>> > >
>> > > echo $PATH
>> > >
>> > >
>> > > If you unzipped it in the $FSLDIR/bin directory, the actual
>> > > executable will be in
>> > >
>> > > $FSLDIR/bin/FSLeyes
>> > >
>> > > if you cd to that directory and type
>> > >
>> > > ./fsleyes
>> > >
>> > > then it should start.
>> > >
>> > >
>> > > you can create a link to the fsleyes program by changing
>> directory
>> > > to $FSLDIR/bin and then
>> > >
>> > > ln -s FSLEYESDIRECTORY/fsleyes fsleyes
>> > >
>> > >
>> > > where FSLEYESDIRECTORY is the directory where fsleyes is. so
>> you
>> > > probably want
>> > >
>> > > ln -s $FSLDIR/bin/FSLeyes/fsleyes fsleyes
>> > >
>> > >
>> > > Hope that helps
>> > >
>> > >
>> > > Michael
>> > >
>> > >
>> > > ------------------------------------------------------------
>> ------------
>> > > *From:* FSL - FMRIB's Software Library <[log in to unmask] <
>> mailto:[log in to unmask] <[log in to unmask]>>
>> > > <mailto:[log in to unmask] <[log in to unmask]>>> on behalf
>> of d m <[log in to unmask]
>> > <mailto:[log in to unmask] <[log in to unmask]>>
>> > > <mailto:[log in to unmask] <[log in to unmask]>>>
>> > > *Sent:* 07 July 2017 18:25
>> > > *To:* [log in to unmask] <mailto:[log in to unmask]
>> <[log in to unmask]>>
>> > <mailto:[log in to unmask] <[log in to unmask]>>
>> > > *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>> > >
>> > > Michael,
>> > >
>> > >
>> > > Thanks for the reply.
>> > >
>> > >
>> > > I'm still somewhat confused. Where exactly do I unzip the
>> folder?
>> > >
>> > >
>> > > Is it the $FSLDIR/bin/ directory?
>> > >
>> > >
>> > > If so, I added the folder and nothing changed.
>> > >
>> > >
>> > > Are there any further steps to complete before using fsleyes?
>> Is
>> > > fslview no longer usable by adding the FSLeyes folder?
>> > >
>> > >
>> > > One thing I noticed, the neurodebian page only shows FSLeyes
>> listed
>> > > for 16.04 and 17.04. Nothing for 14.04? Maybe that is the
>> issue?
>> > >
>> > >
>> > > http://neuro.debian.net/pkgs/fsleyes.html?highlight=fsleyes
>> > <http://neuro.debian.net/pkgs/fsleyes.html?highlight=fsleyes>
>> > > <http://neuro.debian.net/pkgs/fsleyes.html?highlight=fsleyes
>> > <http://neuro.debian.net/pkgs/fsleyes.html?highlight=fsleyes>>
>> > >
>> > >
>> > > Thanks.
>> > >
>> > >
>> > > d.m.
>> > >
>> > > ------------------------------------------------------------
>> ------------
>> > > *From:* FSL - FMRIB's Software Library <[log in to unmask] <
>> mailto:[log in to unmask] <[log in to unmask]>>
>> > > <mailto:[log in to unmask] <[log in to unmask]>>> on behalf
>> of Michael Firbank
>> > > <[log in to unmask] <
>> mailto:[log in to unmask] <[log in to unmask]>>
>> > > <mailto:[log in to unmask]
>> > <mailto:[log in to unmask]
>> <[log in to unmask]>>>>
>> > > *Sent:* Friday, July 7, 2017 10:10:29 AM
>> > > *To:* [log in to unmask] <mailto:[log in to unmask]
>> <[log in to unmask]>>
>> > <mailto:[log in to unmask] <[log in to unmask]>>
>> > > *Subject:* Re: [FSL] fsleyes installation in Ubuntu 14.04
>> > >
>> > > Hello
>> > >
>> > > For 16.04 I just downloaded and unzipped the relevant file
>> from
>> > >
>> > > https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes
>> > <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes>
>> > > <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes
>> > <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes>>
>> > >
>> > > FSLeyes - FslWiki - fsl.fmrib.ox.ac.uk <
>> http://fsl.fmrib.ox.ac.uk>
>> > > <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes
>> > <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes>>
>> > > fsl.fmrib.ox.ac.uk <http://fsl.fmrib.ox.ac.uk>
>> > <http://fsl.fmrib.ox.ac.uk>
>> > > FSLeyes (pronounced fossilise) is the new FSL image viewer,
>> released
>> > > with FSL 5.0.10. FSLeyes can either be installed as a
>> standalone
>> > > application, or can be installed ...
>> > >
>> > > seems to work ok.
>> > >
>> > > Michael
>> > >
>> > > *From:*FSL - FMRIB's Software Library [mailto:
>> [log in to unmask] <mailto:[log in to unmask] <[log in to unmask]>>
>> > > <mailto:[log in to unmask] <[log in to unmask]>>] *On Behalf
>> Of *d m
>> > > *Sent:* 07 July 2017 15:03
>> > > *To:* [log in to unmask] <mailto:[log in to unmask]
>> <[log in to unmask]>>
>> > <mailto:[log in to unmask] <[log in to unmask]>>
>> > > *Subject:* [FSL] fsleyes installation in Ubuntu 14.04
>> > >
>> > > Hello,
>> > >
>> > > How does one install fsleyes with Ubuntu 14.04? We have
>> installed
>> > > fsl using neurodebian.
>> > >
>> > > Thanks.
>> > >
>> > > d.m.
>> > >
>> > >
>> >
>> >
>>
>
>
