Failed to create FSL Python environment in Ubuntu 20.4 shell in Windows 10

Luca

3/3/23, 3:40 PM

I need to use fslreorient2std on some images and I'm trying to install FSL in an Ubuntu 20.04.3 shell in Windows 10.

I used python "/mnt/c/Users/user/Downloads/fslinstaller.py", which seems to work fine until Stage 2 where it produces this error:

...

Stage 2 100% ----- ERROR ----- Failed to create FSL Python environment - see /tmp/fslpython1vkK/fslpython_miniconda_installer.log for details

Post install setup failed [OK] Post installation setup complete Setting up FSL software... [OK] User profile updated with FSL settings, you will need to log out and back in to use the FSL tools.

In fact, when I check the details in "fslpython_miniconda_installer.log" it reads:

Collecting package metadata (repodata.json): ...working... failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/linux-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.

'https://conda.anaconda.org/conda-forge/linux-64'

And indeed even when reopening Ubuntu, FSL commands don't work, for example "fslreorient2std" gives: "/usr/bin/env: 'fslpython': No such file or directory". I did try many times in the last days, following the instructions for Ubuntu, as well as doing the troubleshooting, but the error does not appear intermittent to me. I did not find an answer in stackoverflow as this question¨ does not have an answer and the files mentioned in this thread are not in the corresponding folders in my computer.

Any advice will be welcome, sorry if my question is naive, I'm a new user. Thanks, best L

335

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python

command-line

bash

windows-10

user535733

3/3/23, 4:22 PM

The first step is right there in your output: `Review /tmp/fslpython1vkK/fslpython_miniconda_installer.log for details`

Luca

3/4/23, 5:06 PM

Thanks for your answer, I did check the log and I pasted the relevant details above in my question!

Elon Musk

I sit in a Tesla and translated this thread with Ai:

EN: Failed to create FSL Python environment in Ubuntu 20.4 shell in Windows 10

TH: ไม่สามารถสร้างสภาพแวดล้อม FSL Python ในเชลล์ Ubuntu 20.4 ใน Windows 10

RO: Nu s-a putut crea mediul FSL Python în shell Ubuntu 20.4 în Windows 10

RU: Не удалось создать среду FSL Python в оболочке Ubuntu 20.4 в Windows 10.

VI: Không thể tạo môi trường FSL Python trong vỏ Ubuntu 20.4 trong Windows 10

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