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Dear Stephen and Jon, > Hi - surely it _is_ better to take the individual voxel's > baseline as the denominator in the %change equation; if > the intensity is affected by partial volume, then so > is the activation......? > > Maybe I'm missing something? I try to explain my point a litte bit more formal. Given two volumes V_1 and V_2 sampled at discrete points, in both V_1 and V_2 homologous locations (A_1 and A_2) show the same mean and the same activation effect, where A_1 and A_2 are the only locations showing an activation effect. Let the voxel intensities in V_1 and V_2 around A_1 and A_2 be different. Now apply a spatial convolution L to both V_1 and V_2. Note that the estimated mean intensities in the convolved V_1 and V_2 at voxel A_1 and A_2 will be different, whereas the measured activation effect will not be a function of the intensities around A_1 and A_2. This example can be generalized to a range of other spatial configurations. In other words, relating the signal change to the voxel mean intensity can be misleading, if some low-pass filter L has been applied to the image prior to the statistical analysis. From Jon: > I'm interested in this factor of 8 that is used to provide > a cut-off for signal intensities in GMI calculation, do you > know what the rationale is behind this? You can possibly replace the 8 by any other number as long as it gives you a threshold for roughly segmenting intracranial space. If you like, you could also replace the global mean intensity estimator by your own customized function. > The reason I ask is > that: will this preferentially exclude voxels that are close to > regions of high inhomogeneity (just because their signal intensity > falls within the bottom 12.5%)? The estimate of the global mean intensity will not exclude any voxels from the analysis. However, later on, you (or SPM by default when analyzing fMRI data) choose an analysis threshold. You can easily replace this threshold e.g. by [-inf] such that every voxel survives the mean intensity related threshold. Stefan -- Stefan Kiebel Functional Imaging Laboratory Wellcome Dept. of Cognitive Neurology 12 Queen Square WC1N 3BG London, UK Tel.: +44-(0)20-7833-7478 FAX : -7813-1420 email: [log in to unmask]