Dear FSL experts,
I have just installed FSL 5.0.11 (downloading the installer from the FSL website and instead of running the default command, running the following command: python fslinstaller.py -V 5.0.11). (I need to use this FSL version for some previous analyses)
However, when trying to run eddy_correct the following error appears:
Traceback (most recent call last):
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 583, in _build_master
ws.require(__requires__)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 900, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 791, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (deprecation 2.0 (/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages), Requirement.parse('deprecation<=2.*,>=1.*'), {'fslpy'})
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/fsl//bin/imglob", line 6, in <module>
from pkg_resources import load_entry_point
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3241, in <module>
@_call_aside
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3225, in _call_aside
f(*args, **kwargs)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3254, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 585, in _build_master
return cls._build_from_requirements(__requires__)
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 598, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/pkg_resources/__init__.py", line 786, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'deprecation<=2.*,>=1.*' distribution was not found and is required by fslpy
I followed the advice from https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation
-Check to see if a directory called $FSLDIR/fslpython exists. If it does, delete it.
-Run $FSLDIR/etc/fslconf/fslpython_install.sh -f $FSLDIR to re-install the missing components.
After this, the same error still appeared when runnning eddy_correct
Therefore, following previous messages about the same issue in other users, I downloaded again the fslpython_environment.yml and copied it into $FSLDIR/etc/fslconf/ (overriding the file that is already there).
Then I ran $FSLDIR/etc/fslconf/fslpython_install.sh
I tried again running eddy_correct and now a new error appears:
eddy_correct dti1.nii.gz data 0/usr/local/fsl//bin/eddy_correct: 1: /usr/local/fsl//bin/eddy_correct: /usr/local/fsl//bin/imglob: not found
When I enter in the bin folder from fsl, the imglob file can be opened but is empty. Additionally, the evns folder from fslpython is entirely empty.
What can I do to solve this problem?
Thank you very much in advance,
Agurne
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