Monday, October 29, 2012

SPM Tutorial 1: The Basics

As the majority of neuroimagers use SPM for data analysis, I have begun on another set of introductory tutorials geared toward the beginning SPM user. SPM is what is used in my lab (despite my plugging for AFNI on a regular basis), and while I believe it has its shortcomings - just like any other data analysis package - it has several benefits as well.

Most important, it is run through the Matlab interface. While this may be seen as a hinderance - especially since Matlab is commercial software, thereby making the price of Matlab the price of SPM - I believe that several advantages derive from using Matlab. First, Matlab is an important piece of software that not only serves as the workhorse for SPM, but also allows more complex and sophisticated data analysis, whether that data has been processed in AFNI, FSL, or any other package. Second, while SPM can be used solely through the graphical interface for most purposes, Matlab allows the user to run automated processes from the command line; and a better grasp of the Matlab syntax will make one a better programmer, in addition to strengthening the intuition between what is output to the Matlab terminal and what is being processed within SPM. Last, Matlab's use of matrices provides a clearer link between the raw FMRI data and the operations performed on that data. While Unix can simulate matrices through complex array computations (at least, I think - I've never tried it), the matrices output into Matlab are easier to comprehend and manipulate.

Because of this last point, I believe that SPM has a distinct advantage over the other packages. However, its benefits will disclose themselves only to the diligent, inquiring user who desires to harness the power of Matlab to augment and enhance their data analysis, rather than merely leaving it as a background process to be taken care of by the facade of SPM's graphical user interface. The only drawback is that, for the neuroimager who has been using a bash shell his entire life, learning a new programming environment can be daunting, irritating, and, in some cases, life-threatening. However, there is no need to fear - for those with extensive programming experience, even within one programming language, there are several crossovers into Matlab; and even for programming novitiates, I believe that Matlab can provide a safe, warm, womb-like environment to guide you over the initial hurdles of programming.




By beginning another series on a third software package, one may well ask whether there will ever be any sort of order imposed on this scattering of walkthroughs and tutorials. I admit that I make them more or less as they come to me as I desire, often in thrall of a laudanum-steeped vision; and that it does, in fact, feel as though I am merely binding together several of my most unruly children under one roof. Over the next few months I intend to create a stricter hierarchy for what tutorials should follow which, and I intend to create more ordered playlists that users can click through; but for now, it is an information dump. Partly to help others, yet more often to help me, as I remember material much better if I teach it. But are not the most rewarding acts those which satisfy the needs of all involved?

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