Hi Jeff,

> I've thus got 1 image for each participant and a mixture of categorical and quantitative predictors.

What kind of categorical variables do you have? Between- or within-subject factors? 3dRegAna can handle between-subjects factors, but it would be quite challenging if you have within-subject factors, and that's why you usually recommend 3dMVM in terms of modeling capability and ease of use.

> Does 3dRegAna test every single voxel in the input dataset?

Yes, it's a voxel-wise (or massively univariate) approach.

> does it perform some sort of auto-masking, so that zero-value voxels across most or
> all of the input images are excluded from analysis?

No, it does not.

> shouldn't the presence or absence of a mask affect multiple comparisons correction
> via FDR, 3dClustSim, or some other method?

For FDR, you can run the following command to set the FDR correction with a mask:

3drefit -addFDR -FDRmask ...

3dClustSim also accepts a mask from the user.

Gang