SPM Resources

This page contains links to some helpful SPM resources. If you are aware of any links or documents that could be added, please email them to Terry Oakes (oakes@psyphw.psych.wisc.edu).

External Links:

SPM Central is the primary web resource and home of SPM. If you use SPM much (like, more than once) consider joining the SPM email spewer to keep abreast of recent changes and SPM-related issues. The SPM99 Course Notes at this site are particularly helpful, and provide a moderately in-depth but still readable explanation of the theory behind SPM99. A nice annotated bibliography has been produced by the SPM folks containing an extensive compilation of SPM-related publications. Rik Henson and Wil Penny created a PDF page about ANOVAs.

The MRC-CBU home page contains a wealth of information. The "Site Contents" section has SPM-specific hints, help, and demos. In particular, Matthew Brett has written some very cogent summaries of SPM; look under "Introduction to SPM statistics" and "Introduction to random field theory".

A batch analysis primer by Russ Poldrack from MGH/Harvard. Russ also has a few other potentially helpful documents in the parent directory of the batch analysis primer.

A summary of Random Effects Analysis by Darren Gittelman from Northwestern, with discussions from the SPM-spewer and some references. Also, Eric Zarahn has some interesting online notes.

Various snippets of SPM-related code, compiled by Tom Nichols.

Keck Lab and other local resources:

The Keck Lab's Introduction to SPM99 is available online as an Adobe pdf file. Please send any corrections or suggestions to Terry Oakes.

A primer for fMRI analysis (Adobe .pdf) of a single subject with a simple on/off activation is available. This is actually a modification of the step-by-step guide, together with a real data set, provided by the FIL group (authors of SPM). The primer has been modified to make it specific for the Keck Lab, so that you can follow the primer as you step through the analysis on your own. This is probably the best way to learn how to perform an analysis- by doing it! However, since the analysis has already been run through once, you can also skip the actual processing steps (some of which take an hour or more) and concentrate on the results and analysis.

Another fMRI tutorial is available using a visual stimulation study from the Keck Lab. This page contrasts SPM99's results with a simple subtraction approach, and has a demonstration of why the statistical approach we inflict on ourselves is useful.

Drew Fox has several webpages focused on issues involved in migrating from SPM99 to SPM2b.

Recipe for using SPM's Slice Timing Correction at the Keck Lab, with an example of the results you can expect. This approach is considered outmoded! We currently advocate using AFNI to import images from the scanner after reconstruction, then export the image data in *.img format. This approach will help to keep the orientation of your images the same for your entire study, since AFNI reads the header data of the reconstructed images and knows how to reorient the images to yield a consistent orientation. This is especially important for right/left orientation which can be difficult to ascertain from a particular data set.

Random Effects Analysis discussion.

Matt Budde has some nice tips on batch-mode usage.

Some selected papers, mostly in PDF format:

(alright, we're working on this section- one paper does not quite constitute "some")

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