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