These are two distinct methods of correcting. One, is to synthesize, smooth, analyze, and cluster. The second is to permute, analyze, and cluster. These are realized by two different arguments to the --sim flag in mri_glmfit-sim (either --sim mc-z ... or --sim perm ...)

doug

Chris Hyatt wrote:

I've read both Hagler et al 2006 Neuroimage (Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data) and B. Douglas Ward's description of AlphaSim that both describe clusterwise correction for multiple comparisons.

I recently found, however, an MGH Freesurfer presentation that mentioned that after synthesizing Gaussian noise and smoothing (Monte Carlo), the rows of the design matrix were permuted.

Does the mri_glmfit-sim clusterwise correction method permute rows of the design matrix? I'm still a bit confused about the exact method the clusterwise correction for multiple comparisons work in Freesurfer.

Thanks for your help.

Christopher Hyatt, PhD IOL/Olin Neuropsychiatry Research Center Hartford, CT

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