Frequently Asked Questions - SPM

This set of pages is intended to answer as many common questions about SPM's software quirks as humanly possible. But these pages are not intended to collect everything about SPM - rather, they're intended as a catch-all for SPM questions that don't fall into a theoretical category. If, for example, you have a question about how to do some normalization thing in SPM, check NormalizationHowTos before you tack it onto these pages. You can get a complete listing of the topics that already have FAQs and How-tos at CategoryFaq and CategoryHowTos, respectively.

But if your question doesn't seem to fit any of the categories about analyses already up there... here's the place for you.

Many SPM questions tend to be either of the form, "How do I do x in SPM?" or "My SPM crashed for some x reason - what's the deal?" SpmHowTos and CommonSpmErrors, respectively, are good places for those questions. This FAQ page is intended to be more about general SPM questions - documentation, how to find out more, etc. Good rants are always, of course, welcome.

1. What is SPM? What does it do, exactly?

SPM stands for Statistical Parametric Mapping. And the question of what it's doing can be answered at NutshellSpm. (That page will be edited down shortly and a summary stuck here as well. But it's late right now.)

2. Where can I find some documentation for SPM99?

Well, here, hopefully. :) But if you mean official-type documentation...

The basic, which-button-do-I-push, manual is here:


It doesn't have a lot of info about what exactly SPM is doing, though - just how to make it run.

For help on a particular function in SPM99, the "help" button is often very useful; many of the functions have useful comments at the beginning of their code that is displayed by the "help" button.

You can also check out the archives of the SPM e-mail list (see SpmLinks).

3. Where can I find documentation for SPM2?

Unfortunately, there isn't an "official" manual yet for SPM2. The SPM99 manual above may be somewhat helpful, especially for spatial preprocessing questions; those functions haven't changed a ton between SPM99 and SPM2.

Beyond that, the SPM2 help is a good starting point - many of the functions have helpful comments that will be displayed with its built-in help function. You can access it with the "help" button in the SPM main interface. You can also search the SPM e-mail list archives (see SpmLinks) for a particular question.

4. What's new in SPM2?

Here's a summary of the changes they've made, although some of it's pretty dense:


5. In the SPM data structures, why is the design matrix called xX.X? Why is the filter called K? Why is there a field called SPM.xY.VY? Why are the stimulus functions put in a variable called SPM.Sess.U.u? What does that even mean?

No one knows. Not sure anyone actually writing the software even knows. Possibly a bizarre plot to drive people using SPM insane.

6. What would possess a group writing software to release a highly-anticipated new version of their software and a) make it totally incompatible with any earlier version of their software, to the point of making it actually dangerous to the truth of your results to mix versions and b) changing variable and output names apparently at random from one version to the next with no explanation as to why? Why? Why would someone do such a thing?

See answer to question 5.