Hi Agurne,
I have just discovered an error in the modified
fslpython_environment.yml file that I provided in the other email
thread - you can get a fixed version from here:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;f6ec5ad3.1907
Cheers,
Paul
On 04/07/2019, Agurne Sampedro
<[log in to unmask]> wrote:
> 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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