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Hi William, There is not yet a sraightforwards way of doing this modulation. If I was doing a VBM study with DARTEL, then I would analyse the Jacobian scaled data in the average space of the population, and then map any findings to MNI space. Note that the imported data are rigidly transformed, so that the Jacobians that DARTEL generates should reflect relative volumes (without having to factor in any expansion/contraction from an affine transform). For fMRI, the convention is currently to spatially normalise to MNI space, smooth and then do the stats. There is no Jacobian scaling step in there, and the steps I outlined were really for processing functional data. All the best, -John > I successfully ran dartel on several data sets I have. Thanks again > for the code below. > As I want to report findings in MNI coordinates I followed your > guidelines in dartel_guide.pdf and generated a composite of the > Dartel flow field and the sn.mat file containing the affine > transformation of the template6.nii to the apriori grey.nii and > applied it to the c1*.nii files. > > The next thing I want to do is to modulate the resulting spatial > normalized files. I would preferably be able to modulate "Affine+ > nonlinear" warps and "non-linear" warps only as I would like to look > at the effects of using different schemes for correcting global size > differences. How would I do this??