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Hi Jon, It sounds like they have a different set up to yours. I'm intending to add the "fastest" option back in, but it may take a couple of weeks - if you don't mind, I'll ping you when I have something for you to test. Paul On Mon, 1 Aug 2022 at 16:13, Jon Brooks (PSY - Staff) < [log in to unmask]> wrote: > Hi Paul, > > > > Just wanted to add something else into the mix. > > > > I’ve tried connecting to another site using NoMachine – they are running > the venerable fsleyes 1.1.1, and with best appearance selected for > rendering mode, the system runs as if you were on console – instantly > responsive. I.e. much faster than the latest version with best performance > put back in. > > > > Not sure if this is helpful? Let me know if you want more information > about the setup or indeed if you want to see it in action? > > > > Cheers, Jon > > > > > > Dear Paul, > > > > > > Thanks for this. Seems better, but still not as fast as with previous > version 1.3.3(?) – the default as was distributed with fsl 6.0.5.1 as per > couple of months ago. > > > > > > Followed your instructions to download using git. > > > > > > I needed to “load” fsl in our normal way i.e. module load fsl > > > > Otherwise fslpython isn’t found. > > > > > > (base) [gnx20mmu@uwwbichead01 ~/fsleyes]$ cd fsleyes > > > > (base) [gnx20mmu@uwwbichead01 ~/fsleyes]$ export PYTHONPATH=$(pwd) > > > > (base) [gnx20mmu@uwwbichead01 ~/fsleyes]$ fslpython -m fsleyes -p 1 > > > > > > (40 seconds elapse before splash appears, fslpython showing ~7% CPU usage > during this time). > > > > > > /gpfs/home/gnx20mmu/fsleyes/fsleyes/colourmaps.py:572: UserWarning: Trying > to register the cmap 'pink' which already exists. > > > > mplcm.register_cmap(key, cmap, override_builtin=True) > > > > /gpfs/home/gnx20mmu/fsleyes/fsleyes/colourmaps.py:572: UserWarning: Trying > to register the cmap 'hot' which already exists. > > > > mplcm.register_cmap(key, cmap, override_builtin=True) > > > > /gpfs/home/gnx20mmu/fsleyes/fsleyes/colourmaps.py:572: UserWarning: Trying > to register the cmap 'cool' which already exists. > > > > mplcm.register_cmap(key, cmap, override_builtin=True) > > > > /gpfs/home/gnx20mmu/fsleyes/fsleyes/colourmaps.py:572: UserWarning: Trying > to register the cmap 'copper' which already exists. > > > > mplcm.register_cmap(key, cmap, override_builtin=True) > > > > /gpfs/home/gnx20mmu/fsleyes/fsleyes/colourmaps.py:572: UserWarning: Trying > to register the cmap 'hsv' which already exists. > > > > mplcm.register_cmap(key, cmap, override_builtin=True) > > > > > > (__main__.py:150232): Gtk-CRITICAL **: 21:09:22.638: gtk_window_resize: > assertion 'width > 0' failed > > > > /gpfs/software/ada/fsl/ > 6.0.5.1/fslpython/envs/fslpython/lib/python3.8/site-packages/xnat/__init__.py:27: > DeprecationWarning: the imp module is deprecated in favour of importlib; > see the module's documentation for alternative uses > > > > import imp > > > > /gpfs/software/ada/fsl/ > 6.0.5.1/fslpython/envs/fslpython/lib/python3.8/site-packages/notebook/utils.py:280: > DeprecationWarning: distutils Version classes are deprecated. Use > packaging.version instead. > > > > return LooseVersion(v) >= LooseVersion(check) > > > > > > (__main__.py:150232): Gdk-WARNING **: 21:10:33.640: gdkdrawable-x11.c:952 > drawable is not a pixmap or window > > > > > > Then fsleyes window appears and I’m able to poke around in the standard > brain with a (noticeable) 100ms lag between cursor click and screen update. > > > > > > Relevant?: > > > > I’m running through NoMachine connecting via VPN to server > > The server (CentOS) uses “module” to load fsl (set paths, envars) e.g. > $ module load fsl > > When I start fsleyes python (not fslpython) shows about 10% CPU usage > and the splash takes about 40 seconds to appear, and fsleyes is unusable – > the screen redraws are incredibly slow (2 seconds between each one). > > It’s perfectly possible to watch a youtube video remotely through > NoMachine connection – and glxgears runs smoothly i.e. I don’t think it’s > the connection or the server’s performance > > > > > > So it’s definitely better (x20), but still not great… and not as good as > before. > > > > > > Cheers, Jon > > > > > > > > Hi Jon, > > > > > > I have an experimental version of FSLeyes with the performance setting > added back in. Would you be able to test it on your system to see if it > improves performance? You should be able to use it without modifying your > existing FSL/FSLeyes installation by following these steps: > > > > > > # Clone the git repository, and check out the development branch: > > > > git clone https://git.fmrib.ox.ac.uk/paulmc/fsleyes.git > > > > cd fsleyes > > > > git checkout mnt/revert-remove-performance > > > > > > # Use the PYTHONPATH variable to override the installed FSLeyes version > > > > export PYTHONPATH=$(pwd) > > > > > > # Run fsleyes through the fslpython interpreter, with low performance > enabled > > > > fslpython -m fsleyes -p 1 > > > > > > Paul > > > > > > On Thu, 7 Jul 2022 at 21:26, Jon Brooks (PSY - Staff) <[log in to unmask]> > wrote: > > > > Hi Paul, > > > > > > Thanks for getting back to me – I’m not sure what the issue is, but when > using fsleyes on our headnode (CentOS7) rendering performance in orthoview > is abysmal. We access the server via NoMachine Linux Terminal Server > edition (v6), and the server is using hardware acceleration. > > > > > > In the 1.3.x version we would change performance from Best Appearance to > (Fast or Fastest) and it was like night and day. On the former fsleyes > renders like a download from the 1980s over a dial-up modem, with Fastest > it’s like being sat in front of my mac, instantly responsive, with no > apparent loss of visual quality. > > > > > > So that was a very long winded way of saying: yes please, can we have the > option back 😉 > > > > > > Cheers, Jon > > > > > > -- > > > > Jon Brooks (PSY - Staff) > > > > > > Associate Professor & Head of MRI > > > > University of East Anglia Wellcome Wolfson Brain Imaging Centre (UWWBIC) > > > > School of Psychology, Room 01.56, Lawrence Stenhouse Building, Chancellors > Drive, > > > > Norwich Research Park, Norwich, NR4 7TJ, United Kingdom > > > > Tel: +44(0)1603 591396 > > > > Int: 1396 > > > > A picture containing silhouette Description automatically > generatedsignature_4163963870 > > > > > > UK 14th for Research Quality in Psychology, Psychiatry, and Neuroscience > > > > (Times Higher Education rankings for the Research Excellence Framework > 2021) > > > > World Top 200 (Times Higher Education World University Rankings 2022) > > UK Top 30 (The Times/Sunday Times 2022 and Complete University Guide 2022) > > UK Top 20 for research quality (Times Higher Education Rankings for the > Research Excellence Framework 2021) > > World Top 50 for research citations (Times Higher Education World > University Rankings 2022) > > World Top 50 (Times Higher Education Impact Rankings 2022) > > Athena SWAN Silver Award Holder (since 2019) in recognition of advancement > towards gender equality for all (Advance HE) > > > > > > > > From: Jon Brooks (PSY - Staff) <[log in to unmask]> > > Date: Wednesday, 6 July 2022 at 16:07 > > To: [log in to unmask] <[log in to unmask]> > > Cc: [log in to unmask] <[log in to unmask]> > > Subject: Update to fsleyes 1.4.6 > > > > Hi, > > > > > > We had been having some problems with slow rendering performance on > orthoview, then discovered the rendering performance settings (best > appearance, fast, fastest) – which solved it all…. until now. > > > > > > We just updated to the latest version (1.4.6) and the rendering > performance option under “view settings” (spanner icon) has gone. > > > > > > Any ideas where to start with this one? > > > > > > Cheers, > > > > > > Jon > > > > > > FYI > > > > 1. we’re running on a remote server using NoMachine, with hardware > acceleration turned on > > > > 2. glxgears runs fine > > > > 3. other info below: > > > > > > FSLeyes version: 1.4.6 > > > > FMRIB Centre, Oxford, UK > > > > Paul McCarthy > > > > [log in to unmask] > > > > FSL version: None > > > > FSL directory: /gpfs/software/ada/fsl/6.0.5.1 > > > > OpenGL version: 3.1 > > > > OpenGL compatibility: 2.1 > > > > OpenGL renderer: softpipe > > > > > > FSLeyes was developed at the FMRIB Centre, Nuffield Department of Clinical > Neurosciences, Oxford University, United Kingdom. > > > > > > FSLeyes is a Python application which leverages the following open-source > software libraries: > > > > > > - fsleyes-props [1.7.3] (https://git.fmrib.ox.ac.uk/fsl/fsleyes/props) > > > > - fsleyes-widgets [0.12.3] (https://git.fmrib.ox.ac.uk/fsl/fsleyes/widgets > ) > > > > - fslpy [3.10.0] (https://git.fmrib.ox.ac.uk/fsl/fslpy) > > > > - indexed_gzip [1.6.13] (https://github.com/pauldmccarthy/indexed_gzip/) > > > > - IPython [8.4.0] (https://ipython.org/) > > > > - jinja2 [3.1.2] (http://jinja.pocoo.org) > > > > - Jupyter notebook [6.4.12] (https://jupyter.org) > > > > - matplotlib [3.5.2] (http://www.matplotlib.org) > > > > - nibabel [4.0.1] (http://nipy.org/nibabel) > > > > - numpy [1.22.4] (http://www.numpy.org) > > > > - pillow [9.2.0] (http://python-pillow.org/) > > > > - pyopengl [3.1.6] (http://pyopengl.sourceforge.net) > > > > - pyparsing [2.4.7] (http://pyparsing.wikispaces.com/) > > > > - scipy [1.8.1] (http://www.scipy.org) > > > > - six [1.16.0] (https://pythonhosted.org/six/) > > > > - trimesh [3.12.0] (https://github.com/mikedh/trimesh) > > > > - wxpython [4.1.1] (http://www.wxpython.org) > > > > - wxnatpy [0.4.0] (https://github.com/pauldmccarthy/wxnatpy/) > > > > - xnatpy [0.4.2] (https://bitbucket.org/bigr_erasmusmc/xnatpy) > > > > > > Cubic/spline interpolation routines used in FSLeyes are provided by Daniel > Ruijters and Philippe Thévenaz, described at > http://www.dannyruijters.nl/cubicinterpolation/. > > > > > > The GLSL parser is based on code by Nicolas P . Rougier, available at > https://github.com/rougier/glsl-parser, and released under the BSD > license. > > > > > > Some of the icons used in FSLeyes are derived from the Freeline icon set, > by Enes Dal, available at https://www.iconfinder.com/Enesdal, and > released under the Creative Commons (Attribution 3.0 Unported) license. > > > > > > DICOM to NIFTI conversion is performed with Chris Rorden's dcm2niix ( > https://github.com/rordenlab/dcm2niix). > > > > > > The "brain_colours" colour maps were produced and provided by Cyril Pernet > > > > (https://doi.org/10.1111/ejn.14430). > > > > > > FSLeyes is released under Version 2.0 of the Apache Software License. > Source code for FSLeyes is available at > https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes > > > > > > Copyright 2016-2019 University of Oxford, Oxford, UK. > > > > > > -- > > > > Jon Brooks (PSY - Staff) > > > > > > Associate Professor & Head of MRI > > > > University of East Anglia Wellcome Wolfson Brain Imaging Centre (UWWBIC) > > > > School of Psychology, Room 01.56, Lawrence Stenhouse Building, Chancellors > Drive, > > > > Norwich Research Park, Norwich, NR4 7TJ, United Kingdom > > > > Tel: +44(0)1603 591396 > > > > Int: 1396 > > > > A picture containing silhouette Description automatically > generatedsignature_4163963870 > > > > > > UK 14th for Research Quality in Psychology, Psychiatry, and Neuroscience > > > > (Times Higher Education rankings for the Research Excellence Framework > 2021) > > > > World Top 200 (Times Higher Education World University Rankings 2022) > > UK Top 30 (The Times/Sunday Times 2022 and Complete University Guide 2022) > > UK Top 20 for research quality (Times Higher Education Rankings for the > Research Excellence Framework 2021) > > World Top 50 for research citations (Times Higher Education World > University Rankings 2022) > > World Top 50 (Times Higher Education Impact Rankings 2022) > > Athena SWAN Silver Award Holder (since 2019) in recognition of advancement > towards gender equality for all (Advance HE) > > > > > > > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=FSL&A=1 This message was issued to members of www.jiscmail.ac.uk/FSL, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/