Hi Paul,
Thank you so much for your response. I followed those commands you listed and tested opening FSLeyes again, but after that I’m now unfortunately returning this error:
IC-FVFGN7HQQ05N:~ ah2818$ pwd
/Users/ah2818
IC-FVFGN7HQQ05N:~ ah2818$ sudo rm -r $FSLDIR/fslpython
Password:
IC-FVFGN7HQQ05N:~ ah2818$ sudo $FSLDIR/etc/fslconf/fslpython_install.sh -f $FSLDIR
Password:
Stage 1
By installing this python distribution you agree to the license terms in
/usr/local/fsl/fslpython/LICENSE.txt
100%
Stage 2
100%
/var/folders/yg/glyqxgx114589s22953tdcv80000gp/T/fslpythonXXXX.wbrXIMUa/fslpython_miniconda_installer.log
IC-FVFGN7HQQ05N:~ ah2818$ fsleyes
Traceback (most recent call last):
File "/usr/local/fsl/fslpython/envs/fslpython/bin/fsleyes", line 11, in <module>
sys.exit(main())
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/filtermain.py", line 207, in main
result = fm.main(args)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/main.py", line 243, in main
fsleyes.initialise()
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/__init__.py", line 253, in initialise
plugins.initialise()
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/plugins/__init__.py", line 225, in initialise
_loadBuiltIns()
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/plugins/__init__.py", line 269, in _loadBuiltIns
mod = importlib.import_module(name)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/plugins/controls/filetreepanel/__init__.py", line 18, in <module>
import file_tree
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/file_tree/__init__.py", line 1, in <module>
from .file_tree import FileTree, convert
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/file_tree/file_tree.py", line 5, in <module>
import xarray
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/xarray/__init__.py", line 1, in <module>
from . import testing, tutorial
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/xarray/testing.py", line 9, in <module>
from xarray.core import duck_array_ops, formatting, utils
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/xarray/core/duck_array_ops.py", line 26, in <module>
from . import dask_array_compat, dask_array_ops, dtypes, npcompat, nputils
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/xarray/core/npcompat.py", line 72, in <module>
_SupportsDType[np.dtype],
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/typing.py", line 261, in inner
return func(*args, **kwds)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/typing.py", line 897, in __class_getitem__
_check_generic(cls, params)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/typing_extensions.py", line 95, in _check_generic
raise TypeError(f"{cls} is not a generic class")
TypeError: <class 'numpy.typing._dtype_like._SupportsDType'> is not a generic class
IC-FVFGN7HQQ05N:~ ah2818$
I then closed the terminal and tried again and the original error is showing once more:
IC-FVFGN7HQQ05N:~ ah2818$ fsleyes
Traceback (most recent call last):
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/osmesa.py", line 22, in GL
return ctypesloader.loadLibrary(
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/ctypesloader.py", line 36, in loadLibrary
return _loadLibraryWindows(dllType, name, mode)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/ctypesloader.py", line 89, in _loadLibraryWindows
return dllType( name, mode )
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/ctypes/__init__.py", line 373, in __init__
self._handle = _dlopen(self._name, mode)
OSError: ("dlopen(OSMesa, 0x000A): tried: '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/lib-dynload/../../OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/bin/../lib/OSMesa' (no such file), 'OSMesa' (no such file), '/usr/local/lib/OSMesa' (no such file), '/usr/lib/OSMesa' (no such file), '/Users/ah2818/OSMesa' (no such file)", 'OSMesa', None)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/fsl/fslpython/envs/fslpython/bin/fsleyes", line 11, in <module>
sys.exit(main())
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/filtermain.py", line 207, in main
result = fm.main(args)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/main.py", line 243, in main
fsleyes.initialise()
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/__init__.py", line 243, in initialise
import fsleyes.plugins as plugins
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/plugins/__init__.py", line 196, in <module>
import fsleyes.views.canvaspanel as canvaspanel
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/views/canvaspanel.py", line 20, in <module>
from . import colourbarpanel
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/views/colourbarpanel.py", line 15, in <module>
import fsleyes.gl.wxglcolourbarcanvas as cbarcanvas
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/gl/wxglcolourbarcanvas.py", line 17, in <module>
import fsleyes.gl.colourbarcanvas as cbarcanvas
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/fsleyes/gl/colourbarcanvas.py", line 21, in <module>
import OpenGL.GL as gl
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/GL/__init__.py", line 3, in <module>
from OpenGL import error as _error
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/error.py", line 12, in <module>
from OpenGL import platform, _configflags
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/__init__.py", line 56, in <module>
_load()
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/__init__.py", line 53, in _load
plugin.install(globals())
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/baseplatform.py", line 97, in install
namespace[ name ] = getattr(self,name,None)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/baseplatform.py", line 15, in __get__
value = self.fget( obj )
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/osmesa.py", line 66, in GetCurrentContext
function = self.OSMesa.OSMesaGetCurrentContext
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/baseplatform.py", line 15, in __get__
value = self.fget( obj )
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/osmesa.py", line 60, in OSMesa
def OSMesa( self ): return self.GL
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/baseplatform.py", line 15, in __get__
value = self.fget( obj )
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/site-packages/OpenGL/platform/osmesa.py", line 28, in GL
raise ImportError("Unable to load OpenGL library", *err.args)
ImportError: ('Unable to load OpenGL library', "dlopen(OSMesa, 0x000A): tried: '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/lib-dynload/../../OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/bin/../lib/OSMesa' (no such file), 'OSMesa' (no such file), '/usr/local/lib/OSMesa' (no such file), '/usr/lib/OSMesa' (no such file), '/Users/ah2818/OSMesa' (no such file)", 'OSMesa', None)
IC-FVFGN7HQQ05N:~ ah2818$
Do you have any idea what to do next? Your help is very much appreciated!
Many thanks,
Lexi
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of paul mccarthy <[log in to unmask]>
Date: Friday, 19 August 2022 at 09:11
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] FSLeyes won't run from the command line
This email from [log in to unmask] originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list to disable email stamping for this address.
Hi Lexi,
Have you updated FSLeyes within your FSL installation? In older versions, conda can sometimes make mistakes when generating entry points for Python applications on macOS during an update. This should be resolved in recent versions of conda though (specifically the python.app package).
The easiest option to resolve this is probably to delete and re-install the fslpython conda environment within your $FSLDIR. You should be able to do this by following these steps:
1. Delete the $FSLDIR/fslpython directory:
sudo rm -r $FSLDIR/fslpython
2. Run this script to re-create the fslpython environment:
sudo $FSLDIR/etc/fslconf/fslpython_install.sh -f $FSLDIR
Paul
On Thu, 18 Aug 2022 at 11:47, Hand, Lexi <[log in to unmask]> wrote:
Hi everyone,
I’m having some trouble opening FSLeyes from the command line and keep getting this error:
IC-FVFGN7HQQ05N:~ ah2818$ fsleyes &
[1] 18955
IC-FVFGN7HQQ05N:~ ah2818$ Traceback (most recent call last):
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/osmesa.py", line 22, in GL
return ctypesloader.loadLibrary(
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/ctypesloader.py", line 36, in loadLibrary
return _loadLibraryWindows(dllType, name, mode)
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/ctypesloader.py", line 89, in _loadLibraryWindows
return dllType( name, mode )
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/ctypes/__init__.py", line 373, in __init__
self._handle = _dlopen(self._name, mode)
OSError: ("dlopen(OSMesa, 0x000A): tried: '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/lib-dynload/../../OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/MacOS/../lib/OSMesa' (no such file), 'OSMesa' (no such file), '/usr/local/lib/OSMesa' (no such file), '/usr/lib/OSMesa' (no such file), '/Users/ah2818/OSMesa' (no such file)", 'OSMesa', None)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/fsl/fslpython/envs/fslpython/bin/fsleyes", line 11, in <module>
sys.exit(main())
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/fsleyes/filtermain.py", line 207, in main
result = fm.main(args)
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/fsleyes/main.py", line 243, in main
fsleyes.initialise()
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/fsleyes/__init__.py", line 243, in initialise
import fsleyes.plugins as plugins
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/fsleyes/plugins/__init__.py", line 196, in <module>
import fsleyes.views.canvaspanel as canvaspanel
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/fsleyes/views/canvaspanel.py", line 20, in <module>
from . import colourbarpanel
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/fsleyes/views/colourbarpanel.py", line 15, in <module>
import fsleyes.gl.wxglcolourbarcanvas as cbarcanvas
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/fsleyes/gl/wxglcolourbarcanvas.py", line 17, in <module>
import fsleyes.gl.colourbarcanvas as cbarcanvas
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/fsleyes/gl/colourbarcanvas.py", line 21, in <module>
import OpenGL.GL as gl
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/GL/__init__.py", line 3, in <module>
from OpenGL import error as _error
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/error.py", line 12, in <module>
from OpenGL import platform, _configflags
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/__init__.py", line 36, in <module>
_load()
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/__init__.py", line 33, in _load
plugin.install(globals())
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/baseplatform.py", line 97, in install
namespace[ name ] = getattr(self,name,None)
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/baseplatform.py", line 15, in __get__
value = self.fget( obj )
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/osmesa.py", line 66, in GetCurrentContext
function = self.OSMesa.OSMesaGetCurrentContext
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/baseplatform.py", line 15, in __get__
value = self.fget( obj )
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/osmesa.py", line 60, in OSMesa
def OSMesa( self ): return self.GL
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/baseplatform.py", line 15, in __get__
value = self.fget( obj )
File "/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/lib/python3.8/site-packages/OpenGL/platform/osmesa.py", line 28, in GL
raise ImportError("Unable to load OpenGL library", *err.args)
ImportError: ('Unable to load OpenGL library', "dlopen(OSMesa, 0x000A): tried: '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/python3.8/lib-dynload/../../OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/lib/OSMesa' (no such file), '/usr/local/fsl/fslpython/envs/fslpython/python.app/Contents/MacOS/../lib/OSMesa' (no such file), 'OSMesa' (no such file), '/usr/local/lib/OSMesa' (no such file), '/usr/lib/OSMesa' (no such file), '/Users/ah2818/OSMesa' (no such file)", 'OSMesa', None)
IC-FVFGN7HQQ05N:~ ah2818$
I’ve tried researching but can’t find any solutions. Is anyone able to tell what’s going on and can help me please? It would be very much appreciated!
Many thanks!
Lexi
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