AFNI Command of the Week: 3dinfo

Researchers are always trying to find out more about their data. They examine at it from different angles; place it in their hand and feel its texture and test its heft; and look closely for portents and signs and the apocalypse.

3dinfo, similar to FSL's fslinfo and SPM's spm_vol, returns critical information about an FMRI dataset, such as the number of voxels along the x-, y-, and z-directions, the size of those voxels, and other header essentials, such as the number of volumes and the length of the repetition time (TR). This information is critical when performing steps such as slice timing correction with 3dTshift, when the researcher may want to know more about the number of slices and the acquisition of those slices, or when doing a step like cluster correction, where the voxel dimensions are a critical piece of information.

A few lesser known options include the -VERB option (in all caps), which generates even more information than the typical -verb option, and -echo_edu, which formats the standard output into a clear and easy-to-read table. This and more can be found in the following video:

AFNI Bootcamp: Feburary 25th - March 1st

A spectre is haunting America - The spectre of AFNI. A few times every year the good people at the National Institutes of Health (NIH) hold an AFNI bootcamp at various locations around the country and around the world, attempting to teach, persuade, proselytize, inveigle, and coax young FMRI neophytes into using their product. And, fortunately for the rest of us, sometimes these bootcamps are held at the NIH itself, and these are open to any interested researcher.

I went to one of these bootcamps last spring, and it was an eye-opening, pupil-dilating, sphincter-tightening experience. For five full days we talked about, discussed, and analyzed data; and the nerd bacchanalia continued to rage underneath the carmine streaks of the westering sun. Normalization, connectivity analyses, surface mapping, carousing, bear-baiting, and wenching followed upon these lectures as surely as gout follows upon vice; and although I cannot remember anything that was said or taught during these sessions, I do vividly remember how I felt, which was - kind of sore.

Your ticket to paradise can be found here. Registration tends to fill up very fast, so I recommend submitting an application as soon as possible. Most important, the entire event is free (minus your tax dollars). You will, however, have to pay for your own travel, meals, Nutella, and sketchy Travelodge room.

FSL Tutorial 2: FEAT (Part 1)

A new tutorial about FEAT is now up; depending on how long it takes to get through all of the different tabs in the interface, this may be a three-part series. In any case, this will serve as a basic overview of the preprocessing steps of FEAT, most of which can be left as a default.

The next couple of tutorials will cover the set up of models and timing files within FSL, which can be a little tricky. For those of you who have stuck with it from the beginning (and I have heard that there are a few of you out there: Hello), there will be some more useful features coming up, aside from reviewing the basics.

Eventually we will get around to batch scripting FEAT analyses, which can save you several hours of mindless pointing and clicking, and leave you with plenty of time to watch Starcraft 2 replays, or Breaking Bad, or whatever it is kids watch these days.