Hi Matthew,
Thanks for your response.
I have reverted to an older version since I needed to run some analyses, but I will try that out as soon as I am done with those. I’ll keep you updated whether it worked.
Thanks a lot.
Warmly,
Marie
> On Feb 11, 2020, at 9:31 AM, Matthew Webster <[log in to unmask]> wrote:
>
> Hi Marie,
> As a temporary solution, can you modify
>
> $FSLDIR/etc/fslconf/fslpython_environment.yml
>
> And remove the lines reading:
>
> - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
>
> and
>
> - eddy_qc=1.0.2
>
> And then retry the fslpython installation as before? This should install everything but eddy_qc ( which is hosted on the fslconda channel ). Depending on where you installed the standalone FSLeyes, you might want to move it out of $FSLDIR/bin before installing, as the fslpython environment will attempt to install its own version.
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
>> On 10 Feb 2020, at 13:22, Marie-Eve Hoeppli <[log in to unmask]> wrote:
>>
>> Hi Matthew,
>>
>> Thanks for your answer. I had the same idea for fsleyes and already downloaded it.
>>
>> Please let me know once you find a solution.
>>
>> Thanks a lot.
>>
>> Warmly,
>>
>> Marie
>>
>>> On Feb 10, 2020, at 8:20 AM, Matthew Webster <[log in to unmask]> wrote:
>>>
>>> Hello Marie,
>>> This is certainly the reason why fsleyes isn’t installed ( as a temporary fix, you can download standalone binaries from here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes#Install_standalone_build_.28recommended.29 ). We’re looking into fixes for the SSL problem.
>>>
>>> Kind Regards
>>> Matthew
>>> --------------------------------
>>> Dr Matthew Webster
>>> FMRIB Centre
>>> John Radcliffe Hospital
>>> University of Oxford
>>>
>>>> On 10 Feb 2020, at 13:01, Marie-Eve Hoeppli <[log in to unmask]> wrote:
>>>>
>>>> Hello again,
>>>>
>>>> Is there anything else I can try to solve the error I am getting when I am updating fsl?
>>>>
>>>> Could my issue with fsleyes (not installed after the update) be related to that?
>>>>
>>>> Thanks a lot for your help,
>>>>
>>>> Marie
>>>>
>>>>> On Feb 7, 2020, at 11:40 AM, Marie-Eve Hoeppli <[log in to unmask]> wrote:
>>>>>
>>>>> still getting the same result :(
>>>>>
>>>>> Installing FSL conda distribution into /usr/local/fsl/fslpython
>>>>> % Total % Received % Xferd Average Speed Time Time Time Current
>>>>> Dload Upload Total Spent Left Speed
>>>>>
>>>>> 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
>>>>> 48 49.3M 48 23.9M 0 0 32.3M 0 0:00:01 --:--:-- 0:00:01 32.3M
>>>>> 100 49.3M 100 49.3M 0 0 33.2M 0 0:00:01 0:00:01 --:--:-- 33.2M
>>>>> PREFIX=/usr/local/fsl/fslpython
>>>>> Unpacking payload ...
>>>>>
>>>>> 0%| | 0/35 [00:00<?, ?it/s]
>>>>> Extracting : python.app-2-py37_9.conda: 0%| | 0/35 [00:00<?, ?it/s]
>>>>> Extracting : python.app-2-py37_9.conda: 3%|▎ | 1/35 [00:00<00:13, 2.60it/s]
>>>>> Extracting : six-1.12.0-py37_0.conda: 3%|▎ | 1/35 [00:00<00:13, 2.60it/s]
>>>>> Extracting : libffi-3.2.1-h475c297_4.conda: 6%|▌ | 2/35 [00:00<00:12, 2.60it/s]
>>>>> Extracting : libcxxabi-4.0.1-hcfea43d_1.conda: 9%|▊ | 3/35 [00:00<00:12, 2.60it/s]
>>>>> Extracting : conda-package-handling-1.6.0-py37h1de35cc_0.conda: 11%|█▏ | 4/35 [00:00<00:11, 2.60it/s]
>>>>> Extracting : pycosat-0.6.3-py37h1de35cc_0.conda: 14%|█▍ | 5/35 [00:00<00:11, 2.60it/s]
>>>>> Extracting : ncurses-6.1-h0a44026_1.conda: 17%|█▋ | 6/35 [00:01<00:11, 2.60it/s]
>>>>> Extracting : ncurses-6.1-h0a44026_1.conda: 20%|██ | 7/35 [00:01<00:09, 3.04it/s]
>>>>> Extracting : readline-7.0-h1de35cc_5.conda: 20%|██ | 7/35 [00:01<00:09, 3.04it/s]
>>>>> Extracting : urllib3-1.24.2-py37_0.conda: 23%|██▎ | 8/35 [00:01<00:08, 3.04it/s]
>>>>> Extracting : idna-2.8-py37_0.conda: 26%|██▌ | 9/35 [00:01<00:08, 3.04it/s]
>>>>> Extracting : chardet-3.0.4-py37_1003.conda: 29%|██▊ | 10/35 [00:01<00:08, 3.04it/s]
>>>>> Extracting : zlib-1.2.11-h1de35cc_3.conda: 31%|███▏ | 11/35 [00:01<00:07, 3.04it/s]
>>>>> Extracting : requests-2.22.0-py37_0.conda: 34%|███▍ | 12/35 [00:01<00:07, 3.04it/s]
>>>>> Extracting : ruamel_yaml-0.15.46-py37h1de35cc_0.conda: 37%|███▋ | 13/35 [00:01<00:07, 3.04it/s]
>>>>> Extracting : xz-5.2.4-h1de35cc_4.conda: 40%|████ | 14/35 [00:01<00:06, 3.04it/s]
>>>>> Extracting : libedit-3.1.20181209-hb402a30_0.conda: 43%|████▎ | 15/35 [00:01<00:06, 3.04it/s]
>>>>> Extracting : pycparser-2.19-py37_0.conda: 46%|████▌ | 16/35 [00:01<00:06, 3.04it/s]
>>>>> Extracting : libcxx-4.0.1-hcfea43d_1.conda: 49%|████▊ | 17/35 [00:01<00:05, 3.04it/s]
>>>>> Extracting : yaml-0.1.7-hc338f04_2.conda: 51%|█████▏ | 18/35 [00:01<00:05, 3.04it/s]
>>>>> Extracting : python-3.7.4-h359304d_1.conda: 54%|█████▍ | 19/35 [00:01<00:05, 3.04it/s]
>>>>> Extracting : python-3.7.4-h359304d_1.conda: 57%|█████▋ | 20/35 [00:01<00:03, 4.23it/s]
>>>>> Extracting : pyopenssl-19.0.0-py37_0.conda: 57%|█████▋ | 20/35 [00:01<00:03, 4.23it/s]
>>>>> Extracting : tk-8.6.8-ha441bb4_0.conda: 60%|██████ | 21/35 [00:01<00:03, 4.23it/s]
>>>>> Extracting : tqdm-4.36.1-py_0.conda: 63%|██████▎ | 22/35 [00:01<00:03, 4.23it/s]
>>>>> Extracting : sqlite-3.30.0-ha441bb4_0.tar.bz2: 66%|██████▌ | 23/35 [00:01<00:02, 4.23it/s]
>>>>> Extracting : openssl-1.1.1d-h1de35cc_3.tar.bz2: 69%|██████▊ | 24/35 [00:01<00:02, 4.23it/s]
>>>>> Extracting : pip-19.3.1-py37_0.tar.bz2: 71%|███████▏ | 25/35 [00:01<00:02, 4.23it/s]
>>>>> Extracting : cryptography-2.8-py37ha12b0ac_0.tar.bz2: 74%|███████▍ | 26/35 [00:01<00:02, 4.23it/s]
>>>>> Extracting : conda-4.7.12-py37_0.tar.bz2: 77%|███████▋ | 27/35 [00:01<00:01, 4.23it/s]
>>>>> Extracting : setuptools-41.4.0-py37_0.tar.bz2: 80%|████████ | 28/35 [00:01<00:01, 4.23it/s]
>>>>> Extracting : asn1crypto-1.2.0-py37_0.tar.bz2: 83%|████████▎ | 29/35 [00:01<00:01, 4.23it/s]
>>>>> Extracting : wheel-0.33.6-py37_0.tar.bz2: 86%|████████▌ | 30/35 [00:01<00:01, 4.23it/s]
>>>>> Extracting : ca-certificates-2019.10.16-0.tar.bz2: 89%|████████▊ | 31/35 [00:01<00:00, 4.23it/s]
>>>>> Extracting : cffi-1.13.0-py37hb5b8e2f_0.tar.bz2: 91%|█████████▏| 32/35 [00:01<00:00, 4.23it/s]
>>>>> Extracting : pysocks-1.7.1-py37_0.tar.bz2: 94%|█████████▍| 33/35 [00:01<00:00, 4.23it/s]
>>>>> Extracting : certifi-2019.9.11-py37_0.tar.bz2: 97%|█████████▋| 34/35 [00:01<00:00, 4.23it/s]
>>>>>
>>>>> Collecting package metadata (current_repodata.json): ...working... done
>>>>> Solving environment: ...working... done
>>>>>
>>>>> ## Package Plan ##
>>>>>
>>>>> environment location: /usr/local/fsl/fslpython
>>>>>
>>>>> added / updated specs:
>>>>> - asn1crypto==1.2.0=py37_0
>>>>> - ca-certificates==2019.10.16=0
>>>>> - certifi==2019.9.11=py37_0
>>>>> - cffi==1.13.0=py37hb5b8e2f_0
>>>>> - chardet==3.0.4=py37_1003
>>>>> - conda-package-handling==1.6.0=py37h1de35cc_0
>>>>> - conda==4.7.12=py37_0
>>>>> - cryptography==2.8=py37ha12b0ac_0
>>>>> - idna==2.8=py37_0
>>>>> - libcxx==4.0.1=hcfea43d_1
>>>>> - libcxxabi==4.0.1=hcfea43d_1
>>>>> - libedit==3.1.20181209=hb402a30_0
>>>>> - libffi==3.2.1=h475c297_4
>>>>> - ncurses==6.1=h0a44026_1
>>>>> - openssl==1.1.1d=h1de35cc_3
>>>>> - pip==19.3.1=py37_0
>>>>> - pycosat==0.6.3=py37h1de35cc_0
>>>>> - pycparser==2.19=py37_0
>>>>> - pyopenssl==19.0.0=py37_0
>>>>> - pysocks==1.7.1=py37_0
>>>>> - python.app==2=py37_9
>>>>> - python==3.7.4=h359304d_1
>>>>> - readline==7.0=h1de35cc_5
>>>>> - requests==2.22.0=py37_0
>>>>> - ruamel_yaml==0.15.46=py37h1de35cc_0
>>>>> - setuptools==41.4.0=py37_0
>>>>> - six==1.12.0=py37_0
>>>>> - sqlite==3.30.0=ha441bb4_0
>>>>> - tk==8.6.8=ha441bb4_0
>>>>> - tqdm==4.36.1=py_0
>>>>> - urllib3==1.24.2=py37_0
>>>>> - wheel==0.33.6=py37_0
>>>>> - xz==5.2.4=h1de35cc_4
>>>>> - yaml==0.1.7=hc338f04_2
>>>>> - zlib==1.2.11=h1de35cc_3
>>>>>
>>>>>
>>>>> The following NEW packages will be INSTALLED:
>>>>>
>>>>> asn1crypto pkgs/main/osx-64::asn1crypto-1.2.0-py37_0
>>>>> ca-certificates pkgs/main/osx-64::ca-certificates-2019.10.16-0
>>>>> certifi pkgs/main/osx-64::certifi-2019.9.11-py37_0
>>>>> cffi pkgs/main/osx-64::cffi-1.13.0-py37hb5b8e2f_0
>>>>> chardet pkgs/main/osx-64::chardet-3.0.4-py37_1003
>>>>> conda pkgs/main/osx-64::conda-4.7.12-py37_0
>>>>> conda-package-han~ pkgs/main/osx-64::conda-package-handling-1.6.0-py37h1de35cc_0
>>>>> cryptography pkgs/main/osx-64::cryptography-2.8-py37ha12b0ac_0
>>>>> idna pkgs/main/osx-64::idna-2.8-py37_0
>>>>> libcxx pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
>>>>> libcxxabi pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
>>>>> libedit pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
>>>>> libffi pkgs/main/osx-64::libffi-3.2.1-h475c297_4
>>>>> ncurses pkgs/main/osx-64::ncurses-6.1-h0a44026_1
>>>>> openssl pkgs/main/osx-64::openssl-1.1.1d-h1de35cc_3
>>>>> pip pkgs/main/osx-64::pip-19.3.1-py37_0
>>>>> pycosat pkgs/main/osx-64::pycosat-0.6.3-py37h1de35cc_0
>>>>> pycparser pkgs/main/osx-64::pycparser-2.19-py37_0
>>>>> pyopenssl pkgs/main/osx-64::pyopenssl-19.0.0-py37_0
>>>>> pysocks pkgs/main/osx-64::pysocks-1.7.1-py37_0
>>>>> python pkgs/main/osx-64::python-3.7.4-h359304d_1
>>>>> python.app pkgs/main/osx-64::python.app-2-py37_9
>>>>> readline pkgs/main/osx-64::readline-7.0-h1de35cc_5
>>>>> requests pkgs/main/osx-64::requests-2.22.0-py37_0
>>>>> ruamel_yaml pkgs/main/osx-64::ruamel_yaml-0.15.46-py37h1de35cc_0
>>>>> setuptools pkgs/main/osx-64::setuptools-41.4.0-py37_0
>>>>> six pkgs/main/osx-64::six-1.12.0-py37_0
>>>>> sqlite pkgs/main/osx-64::sqlite-3.30.0-ha441bb4_0
>>>>> tk pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
>>>>> tqdm pkgs/main/noarch::tqdm-4.36.1-py_0
>>>>> urllib3 pkgs/main/osx-64::urllib3-1.24.2-py37_0
>>>>> wheel pkgs/main/osx-64::wheel-0.33.6-py37_0
>>>>> xz pkgs/main/osx-64::xz-5.2.4-h1de35cc_4
>>>>> yaml pkgs/main/osx-64::yaml-0.1.7-hc338f04_2
>>>>> zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3
>>>>>
>>>>>
>>>>> Preparing transaction: ...working... done
>>>>> Executing transaction: ...working... done
>>>>> installation finished.
>>>>> Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you.
>>>>> Collecting package metadata (repodata.json): ...working... failed
>>>>>
>>>>> CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel/osx-64/repodata.json>
>>>>> Elapsed: -
>>>>>
>>>>> An HTTP error occurred when trying to retrieve this URL.
>>>>> HTTP errors are often intermittent, and a simple retry will get you on your way.
>>>>> SSLError(MaxRetryError('HTTPSConnectionPool(host=\'fsl.fmrib.ox.ac.uk\', port=443): Max retries exceeded with url: /fsldownloads/fslconda/channel/osx-64/repodata.json (Caused by SSLError(SSLError("bad handshake: Error([(\'SSL routines\', \'tls_process_server_certificate\', \'certificate verify failed\')])")))'))
>>>>>
>>>>> ########################################################################
>>>>>
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>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>>
>>>>
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>>>>
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>>>
>>>
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>>
>>
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>
>
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>
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