Hi Barbara,
have you tried to turn on compression (ssh -X -C ...)?
A tool that I use quite often in such situations is sshfs. Using sshfs,
you can run FSLeyes/FSLView or any other application locally while still
being able to conveniently access remote data. At the same time, you
avoid the significant network traffic overhead caused by X11 forwarding.
There will still be an initial delay upon loading/opening remote data
but in my experience things work smoothly after that.
If this is an option for you, try this:
$ mkdir -p ~/mnt/host
$ sshfs user@host:/ ~/mnt/host -o idmap=user
$ fsleyes
~/mnt/host/volatile2/neuroimaging/applications/fsl/data/standard/FMRIB58_FA_1mm.nii
Cheers,
Kris
On 03.11.2017 16:59, paul mccarthy wrote:
> Hi Barbara,
>
> It sounds like the network connection is your bottleneck - no
> applications are going to run fast. You will get better performance by
> using something other than SSH/X11 - does your institution have VNC? Or
> can you download the data and view it locally?
>
> Cheers,
>
> Paul
>
> On 3 November 2017 at 12:33, Barbara Kreilkamp
> <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Thank you very much, Paul.
>
> I just tried it out again with a faster internet connection (2MBPS).
>
> Here is how FSLView and FSLEYES compare:
>
> fslview_deprecated
> /volatile2/neuroimaging/applications/fsl/data/standard/FMRIB58_FA_1mm.nii
>
>
> This command takes 4 minutes to load the FA image and it takes 20
> seconds to jump to another slice.
>
> fsleyes
> /volatile2/neuroimaging/applications/fsl/data/standard/FMRIB58_FA_1mm.nii
> libGL error: No matching fbConfigs or visuals found
> libGL error: failed to load driver: swrast
>
> This command takes 23 minutes to load the FA image and it takes 17
> seconds to jump to another slice. Does the error have anything to do
> with it? (I don't get this when I use FSLView)
>
>
> Best wishes,
>
> Barbara
>
>
> On 30/10/2017 12:49, paul mccarthy wrote:
>> Hi Barbara,
>>
>> Performance over a SSH connection is dependent on the quality of
>> the network connection. How does FSLeyes compare with other
>> graphical applications (e.g. FSLView)?
>>
>> Cheers,
>>
>> Paul
>>
>> On 29 October 2017 at 17:34, Barbara Kreilkamp
>> <[log in to unmask]
>> <mailto:[log in to unmask]>> wrote:
>>
>> It appears, if I wait long enough (FSLEyes version 0.15.1),
>> that the FA image does load completely. But it really takes a
>> long time.
>>
>> Is there a way to speed things up or does the warning below
>> have anything to do with it?
>>
>> Thanks again,
>>
>> best wishes,
>>
>> Barbara
>>
>>
>> libGL error: No matching fbConfigs or visuals found
>> libGL error: failed to load driver: swrast
>>
>>
>>
>>
>> On 29/10/2017 16:54, Barbara Kreilkamp wrote:
>>>
>>> Thank you Paul,
>>>
>>> Okay, I will use ssh -Y then to connect. FSLeyes works to
>>> some degree in scenario (1), it loads itself, and all the
>>> options, but rather slowly...
>>>
>>> However, I tried loading in the JHU FA image and that does
>>> not show up, although the dimension information etc. is
>>> loaded from the image but I cannot actually see the FA image
>>> or its values.
>>>
>>> Thanks again,
>>>
>>> Best wishes,
>>>
>>> Barbara
>>>
>>>
>>>
>>>
>>>
>>> On 28/10/2017 16:24, paul mccarthy wrote:
>>>> Hi Barbara,
>>>>
>>>> In the first scenario (ssh -Y), does FSLeyes actually work?
>>>> If it does, you can safely ignore those error messages.
>>>>
>>>> The errors in the second scenario (ssh -X) are probably to
>>>> do with the configuration of the SSH server on your cluster,
>>>> rather than being something specific to FSL. I am guessing
>>>> that no GUI applications will work for you, when connecting
>>>> via ssh -X.
>>>>
>>>> Cheers,
>>>>
>>>> Paul
>>>>
>>>>
>>>>
>>>> On 27 October 2017 at 20:16, Barbara Kreilkamp
>>>> <[log in to unmask]
>>>> <mailto:[log in to unmask]>> wrote:
>>>>
>>>> Dear FSL experts,
>>>>
>>>> I have just downloaded the newest version of FSL 5.0.10.
>>>> on the Centos 6 university cluster. I remotely call the
>>>> application from the cluster from my host computer ->
>>>> MAC OSX high Sierra. I also installed FSL 5.0.10 on this
>>>> Mac, and it works fine. So the display issues I am
>>>> having from the remote connection must be the login ssh
>>>> issue or the X11 application.
>>>>
>>>> I have tried to launch the User interface - in some
>>>> cases (when I type ssh -Y when logging in, the user
>>>> interface 'fsl' kind of works (see (1) - but without
>>>> FSLEYES working properly), but when I type ssh -X I get
>>>> odd display error messages (see (2)) and nothing works.
>>>>
>>>> I am wondering if there is any fix to this? Also the
>>>> user interface is kind of slow to respond - this may be
>>>> because I am using an older version of X11 (2.7.7) - I
>>>> couldn't get XQuartz to start up (2.7.11), although I
>>>> installed both. These were the instructions I wrote
>>>> while following these steps:
>>>>
>>>> # Install X11 (2.7.7) on your machine running OSX high
>>>> Sierra (OS 10.13) - go under X11 preferences and enable
>>>> everything. Then log in as described above. type fsl to
>>>> test. Really we should install the latest X11
>>>> application -> XQuartz (2.7.11), but this does not work
>>>> with FSL/Freesurfer etc. right now.
>>>>
>>>> Any help is greatly appreciated.
>>>>
>>>> All the best wishes,
>>>>
>>>> Barbara
>>>>
>>>>
>>>>
>>>> (1) FSLEYES display issues (after FSL starts fine after
>>>> ssh -Y)
>>>>
>>>> fsl
>>>> libGL error: No matching fbConfigs or visuals found
>>>> libGL error: failed to load driver: swrast
>>>> WARNING numpymodule.py 30: <module> -
>>>> Unable to load numpy_formathandler accelerator from
>>>> OpenGL_accelerate
>>>>
>>>>
>>>> (2) General Display Issues (when launching with ssh -X)
>>>>
>>>> fsl
>>>> Application initialization failed: couldn't connect to
>>>> display "localhost.10.0"
>>>> Error in startup script: couldn't connect to display
>>>> "localhost.10.0"
>>>> while executing
>>>> "load
>>>> /volatile2/neuroimaging/applications/fsl/extras/lib/libtk8.4.so
>>>> <http://libtk8.4.so> Tk"
>>>> ("package ifneeded" script)
>>>> invoked from within
>>>> "package require Tk"
>>>> invoked from within
>>>> "if { [ string match -nocase *wish* $MYSHELL ] } {
>>>> package require Tk
>>>> # tk_focusFollowsMouse
>>>> #bind Button <Enter> { focus %W ; tk::ButtonEnter ..."
>>>> (file
>>>> "/volatile2/neuroimaging/applications/fsl/tcl/fslstart.tcl"
>>>> line 18)
>>>> invoked from within
>>>> "source [ file dirname [ info script ] ]/fslstart.tcl"
>>>> (file
>>>> "/volatile2/neuroimaging/applications/fsl/tcl/fsl.tcl"
>>>> line 71)
>>>> invoked from within
>>>> "source ${FSLDIR}/tcl/${origname}.tcl"
>>>> (file
>>>> "/volatile2/neuroimaging/applications/fsl/bin/fsl" line 22)
>>>>
>>>>
>>>
>>
>>
>
>
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