FSL Version 5 in Mountain Lion

I just upgraded to FSL version 5 on my MacBook Pro running Mountain Lion. The installation was straightforward using the new install script from FMRIB: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation

Download the python script and then in Terminal navigate to the download location and run: python fslinstaller.py

That will download the files and then install FSL with minimal user interaction (you can specify an installation path – on a single user computer it’s fine to use the default path, on shared computers, I find a better install path is something like /usr/share).

If you are running OS X 10.8 (Mountain Lion), you need to install XQuartz (you need an X11 environment regardless of the version of OS X you are running): http://xquartz.macosforge.org/landing/. This version of XQuartz works with OS X 10.6 and later (and is what you have to install with Mountain Lion).

Now everything should be set up to run FSL 5 on a Mac running OS X 10.8. I’ve not run into any problems so far. Thanks to FMRIB, installation of FSL is now easier than it already was.

About Jared Tanner

I have a PhD in Clinical and Health Psychology with an emphasis in neuropsychology at the University of Florida. I previously studied at Brigham Young University. I am currently a Research Assistant Professor at the University of Florida. I spend the bulk of my research time dealing with structural magnetic resonance images of the brain. My specialty is with traditional structural MR images, such as T1-weighted and T2-weighted images, as well as diffusion weighted images. I also look at the cognitive and behavioral functioning of individuals with PD and older adults undergoing orthopedic surgery. Funding for the images came from NINDS K23NS060660 (awarded to Catherine Price, University of Florida). Brain images may not be used without my written permission (grant and software requirements).
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