Tuesday, September 18, 2012


Yesterday I was surprised to find AFNI message boards linking to my first blog post about AFNI. I felt as though the klieg lights had suddenly been turned on me, and that hordes of AFNI nerdlings would soon be funneled into this cramped corner of cyberspace. If you count yourself among their number, then welcome; I hope you enjoy this blog and find it useful.

However, there are a few disclaimers I should state up front:

  1. I do not work for AFNI; I am merely an enthusiastic amateur. If you post any questions either on this blog or on Youtube I will be more than willing to answer them. However, if it is something over my head that I can't answer, then I will suggest that you try the official AFNI message board - it is policed 24/7 by the AFNI overlords, and they will hunt down and answer your questions with terrifying quickness.
  2. I am by no means an AFNI or fMRI expert; as far as you're concerned, I could be an SPM saboteur attempting to lead you astray. When I write about something, you should do your own research and come to your own conclusions. That being said, when I do post about certain topics I try to stick to what I know and to come clean about what I don't know. I hope you can appreciate that, being a guy, this is difficult for me.
  3. This blog is not just about AFNI and fMRI; it is about my brain - it is about life itself. I reserve the right to post about running, music, Nutella, Nutella accessories (including Graham-cracker spoons), books, relationship advice, and other interests. If you have a request about a certain topic, then I will be happy to consider it; however, do not expect this blog to be constrained to any one topic. Like me, it is broad. It sprawls. If you come desiring one thing and one thing only, you will be sorely disappointed; then shall you be cast into outer darkness, and there will be a wailing and gnashing of teeth.

My goal is to identify, target, and remove needless obstacles to understanding. As I have said before, the tutorials are targeted at beginners - though eventually we may work our way up to more sophisticated topics - and I try to present the essential details as clearly as possible. As you may have noticed at some point during your career, there are an elite few who have never had any trouble understanding fMRI analysis; they are disgusting people and should be avoided. For the rest of us, we may require additional tools to help with the basics; and I hope that the tutorials can help with that.

Good luck!


  1. Dear Andy,
    I am an Italian neuroradiology researcher (permanent fellow) and write to express all my solidarity with you.
    I am really sorry for what happened to you yesterday.
    I recently participated to an FSL course (Auckland course, May 2012) and found your tutorials really very very helpful for a beginner like me.
    I truly hope you’ll continue to post “your brain” on your website.
    Good luck from a grateful person
    Daniela Cevolani

    1. Daniela,

      Thank you so much for the kind words! However, I am not complaining that AFNI provided a link to the blog; on the contrary, it is a cause for celebration. The greater the number who find this a useful resource, the greater my joy.

      Please let me know if there is anything in particular that you would like to learn more about; as yet, I have only covered the basics of FSL, for that is as much as I know. However, I also like to hear about what others are interested in.

      Good luck to you as well!


    2. Dear Andy.
      Thank you for your kindness and helpfulness.

      Since you asked me, I’ll avail myself of such opportunity immediately.

      I’d like to know something more about FSL resting state, probabilistic tractography and Freesurfer integration of fMRI and DTI FSL results.
      I realize that in a few words I asked a lot, but do what you can.

      Anyhow, thank you in advance.

      All the best

      PS. Once again, congratulations for your useful website!

    3. Hi Daniela,

      My knowledge of FSL is not that advanced, but I have done Freesurfer integration of fMRI results - just not with FSL! However, I may get to that at some point in the future.

      Thanks again,


    4. Hi Andy,
      Thank you for your answer and interest.
      Any “piece” of “your brain” you will post on your website about this subject will be welcome.