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VBM

Preprocessing

Create the mean T1, coregister to the MNI T1 template.

Use the SPM5 "Segment." Data will be your T1 scans (you can enter multiple subjects in different folders, but make sure you only have one T1 per subject). Output files for gray and white matter should be at least "Modulated + Unmodulated Normalised" and I would recommend "Native + Modulated + Unmodulated" (native files can be used to check the segmentation). For CSF you don't need the Modulated files (the native and unmodulated files can interesting for seeing where CSF is. Save bias corrected, and use thorough clean-up.

Smooth (typically 12 FWHM, but can use 10) the "density" or 'modulated files: "density" files are prepended with "wc1" (gray matter) or "wc2" (white matter). The modulated files are prepended with "mwc1" or "mwc2."

Statistics

The files used for analysis can be the smoothed density or modulated images (prepended with "swc1" or smwc1").

So set up a model, go to SPM Statistical Analysis.

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