SPM vs. FSL by Chris Rorden, and some miscellaneous fMRI tips

I’ve noticed that my previous postings (here and here) about the differences between popular bits of neuroimaging software have been pretty popular in terms of traffic, so I thought I’d just point you towards a similar powerpoint presentation I’ve just found authored by Chris Rorden. It’s fairly brief, but does contain a lot of good information about the key differences between FSL and SPM, particularly in terms of their different approaches to spatial normalisation and  You can download the .ppt file here.

For those who might already be a bit more advanced in their practice of the dark art of fMRI analysis, Chris also has an great set of scripts for SPM8 here, plus of course, his MRICron software is outstandingly useful.

Finally, for FSL users (see – something for everyone at this blog!) I have this little tip, from the mysteriously-named “neuroimager”, which is a fantastic and beautiful method of displaying functional results on a 3D-rendered brain image, using freesurfer.


About Matt Wall

I do brains. BRAINZZZZ.

Posted on February 28, 2012, in Experimental techniques, Neuroimaging, Software and tagged , , , , , . Bookmark the permalink. 5 Comments.

  1. I read your SPM v FSL comparison ppt. It was a helpful intro. I was hoping you could provide more advice. I’m a clinical psychology PhD student who studies the neurobiological underpinnings of traumatic stress. I do not know any imaging packages but will now start. I am trying to decide between FSL and SPM. I know SPM is the most used package, but it seems FSL is dominant in SPM–though I am not sure that is accurate. I’m pretty new to this imaging stuff. Given the brief background I provided, would you be able to tell me what way, in your opinion, is the best way to go? FSL? SPM? Another software?

    • Hi Julia,
      This is always a tricky question, as there is no ‘best’ answer really. Both packages are pretty mature now, and both are very good in their own way.

      The best advice I have on this is to go with whatever system others are using in your institution. Learning these things is hard on your own, but it’s much easier if you have other people around you who are using them, with whom you can discuss issues and ask questions. If you know people who are using FSL, then use FSL.

      Other considerations are the kind of systems you have – for instance, FSL will only run on Unix, and SPM will only run on Matlab (i.e. requires a Matlab licence). For instance, if your lab uses Windows, but already has Matlab licences, then SPM is an obvious choice.

      Both systems have their quirks and advantages… Be assured that because there is no ‘right’ choice, there is also no ‘wrong’ choice either! Whichever you choose will almost certainly be able to do what you want.

      Hope that helps!


  2. Are there any other docs/links that provides comprehensive comparison between different methods(SPM, FSL,FreeSurfer,AFNI,BG) ?

  1. Pingback: The effects of hardware, software, and operating system on brain imaging results « Computing for Psychologists

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