Problems installing FSL

Software Support
104

Hi @paulmccarthy, Yes, I tried installing Miniconda directly and got the same error. I will contact my IT department and see what we can do. Thanks for troubleshooting!

105

After successful installation of FSL in ubuntu 22.04,
echo

$FSLDIR

is showing blank space
and

pc@pc-MS-7D88:~ flirt --version

Command ā€˜flirtā€™ not found, did you mean:
command ā€˜flistā€™ from deb mmh (0.4-4)
command ā€˜flistā€™ from deb nmh (1.7.1-11)
command ā€˜flitā€™ from deb flit (3.6.0-1)
Try: sudo apt install
i have used the command
:~$ python fslinstaller.py
Path is set to this

FSL Setup

FSLDIR=/home/pc/fsl
PATH={FSLDIR}/share/fsl/bin:{PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh

Please help

106

Hi @Priyanka_Chakraborty, did you close your terminal and open a new one after the installation completed?

What is the output of running echo $SHELL, and what file was the FSL initialisation code saved to (e.g. ~/.zshrc, ~/.profile, etc)?

107

Dear Eurostars,

I previously downloaded FSL, but after upgrading to Mac SONOMA, I accidentally (mistakenly) removed the existing FSL and had to reinstall it. However, at 3/3, it never changes from 0%. I tried all previously discussed commands, but nothing worked.
The last command I tried is: python fslinstaller.py --miniconda https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
it gives me an error.

You can see my log file here:

I attached the screen shot below.

Screenshot 2024-09-10 at 8.11.26 PM
Screenshot 2024-09-10 at 8.11.26 PM1630Ɨ1434 175 KB

Thanks for your help.

108

Hi @Ji_Won_Bang, have you tried using the system python, rather than your anaconda python? e.g.:

/usr/bin/python fslinstaller.py
109

Hi @paulmccarthy

Thanks for your suggestion.
When I typed:
/usr/bin/python fslinstaller.py
It says:
zsh: no such file or directory: /usr/bin/python

So I tried:
cd ~/Downloads
python fslinstaller.py

And I got the same error.
Please see log here:

Screenshot is attached below:

Screenshot 2024-09-11 at 11.18.03 AM
Screenshot 2024-09-11 at 11.18.03 AM1326Ɨ1056 120 KB

Please help me! Thanks!

111

Hi @Ji_Won_Bang, Iā€™d like to know whether the installer works with a python interpreter which is not from your anaconda installation. Do you have another python interpreter on your system? Other common paths to try are:

  • /usr/bin/python3 (system)
  • /usr/local/bin/python (homebrew)
  • /Library/Frameworks/Python.Framework/3.<X>/bin/python3 (installed from python.org, replacing <X> with the specific minor version)

If you donā€™t have any of the above, you can try installing a version of Python from https://www.python.org/. Make sure to follow the instructions regarding the Install certificates command, otherwise you may encounter TLS/SSL errors. Also note that the Python installer may add itself to the beginning of your $PATH, which you will need to adjust afterwards in your shell profile, if you would prefer to keep your anaconda installation as the default Python installation.

112

Hi. @paulmccarthy

Thanks for your suggestion!
I do have python interpreter at /usr/bin/python3
So I typed: /usr/bin/python3 fslinstaller.py
And at the stage 3, the installation progress stays at 0% for more than 10 hours up to now.
Should I let it continue its work? Or does it mean itā€™s not working?
When I checked the memory size thatā€™s available, it continues to decline though itā€™s slow. So I thought the installation process is still going on.
Please do let me know what I should do!

Thanks so much!