Installing FSL

Register here: https://fsl.fmrib.ox.ac.uk/fsldownloads_registration/

• this will get you the fslinstaller.py for your Operating System (OS)

Follow instructions here, for example for MacOSX

• https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/MacOsX
• video: https://www.youtube.com/watch?v=QNp3lyP57rw

If you get errors in usage:

In June 2020, MV ran into this issue: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind2004&L=FSL&D=0&P=73952

And these are commands used to fix it:

Open fslpython_install.sh with this command in the terminal (sudo is giving you super permissions to edit really important files, so use sparingly): sudo pico /usr/local/fsl/etc/fslconf/fslpython_install.sh

In pico or nano, use your cursor to move down to line 149 (in pico press ctrl +C to see the line numbers) Line 149 currently reads: dl_cmd_opts="--fail" Change it to: dl_cmd_opts="--fail -L"

In pico/nano press Ctrl + O to write out and save your changes, and then exit pico.

In the terminal then paste the following at the command prompt to re-install fslpython: sudo /usr/local/fsl/etc/fslconf/fslpython_install.sh -f /usr/local/fsl type bash at the terminal to reinstate fsl, and then type imglob to see if you now see imglob usage