Problem installing FSL

Software Support
42

Hi @Tiying, I’m afraid your OS is too old - Apple stopped supporting this OS over four years ago. You’ll have to upgrade your OS/machine*, or install an older version of FSL.

I’m on holiday at the moment, and don’t have access to a mac, so I’m not exactly sure what version of FSL will install on High Sierra, but you could try e.g.:

python fslinstaller.py -V 6.0.7

The full list of FSL releases can be found here.

Alternatively, if you don’t need the MIST sub-cortical segmentation tool, you may be able to install the latest version of FSL with a command such as:

python fslinstaller.py \
  --exclude_package fsl-mist \
  --exclude_package vtk-base \
  --exclude_package wxwidgets \
  --exclude_package wxpython

This command is untested, so there may be other dependencies that are not compatible with your OS. If the installation still fails, please share the log file and I can try and suggest an alternative.

You should not need to use the --conda option at all.

*You can blame Apple for this situation.

43

Thank you very much Paul @paulmccarthy ! I will try to either upgrade my Mac system, or I will use the codes you suggested to download an old version FSL! Hope you have a nice holiday!

44

Hi @paulmccarthy , I tried to download, Version 6.0.5 was successfully downloaded. But in the process of installation, there is no progress in Stage 2, it always appear 1% and no change in two hours. I wonder if it is because my machine (Mac High Sierra 10.13.6) is too old, or other potential reasons? Can I please ask for some advice in this situation? Thank you so much. I attached the code:
Checking FSL package

[OK] File downloaded

Installing FSL software version 6.0.5.2…

FSL exists in the current location, would you like to keep a backup of the old version (N.B. You will not be able to use the old version)? [no]: no

We require your password to continue…

password:

[OK] FSL software installed.

Performing post install tasks

Checking for X11 windowing system (required for FSL GUIs).

[OK] X11 (required for GUIs) found

Stage 1

By installing this python distribution you agree to the license terms in

/usr/local/fsl/fslpython/LICENSE.txt

100%

Stage 2

1%

45

Hi @Tiying, did you try the command that I suggested, to get the latest version? It seems to be working for me:

python fslinstaller.py \
  --exclude_package fsl-mist \
  --exclude_package vtk-base \
  --exclude_package wxwidgets \
  --exclude_package wxpython
46

Hi @paulmccarthy I tried today and it finally downloaded and installed successfully. So happy to see the FSL interface working finally! Thank you for your help and making my day

47

Hi guys, maybe it will help somebody with Linux (Ubuntu 24).
For me the file downloaded from here: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py worked perfectly when I run just python3 fslinstaller.py.

The issue I had:
This command returned an error: /home/ubuntu/fsl/bin/micromamba env update -p /home/ubuntu/fsl -f fsl-6.0.7.17_linux-64.yml --rc-file /home/ubuntu/fsl/.condarc

I fixed it by setting up a brand new machine with Ubuntu 22.04. It seems like the installer doesn’t work on Ubuntu 24.

48

Hi @pawel.szwajnoch, FSL can be installed just fine on Ubuntu 24.04 - there must be another reason as to why it was failing for you.

49

Hmm maybe but I’ve got the same error like the guys above (on an fresh clear VM so it’s hard to detect an issue on my end) and just changing the Ubuntu helped for me :smile:

50

@pawel.szwajnoch If you can share the log file from a failed installation, then I can give further advice.