Hello, as you are probably analysing modulated data in the GLM, that is local volumes, it definitely makes sense to correct for total intracranial volume, or total gray matter volume. Both TIV and total GM should be calculated from the modulated normalised images, yes, as only these represent actually *volumes*. (Alternatively the sum of native probability maps of GM, WM and CSF can be used which should give exactly the same values). Thresholding modulated maps: as you write, at first sight, it may see odd and not logical to threshold the modulated volume maps. However, as they are based on probability maps that are then corrected by JM for the warping effects, very low probabilities may represent not so valid estimations, arguing for a thresholding step to neglect those low prob voxels. As long as the same rule is applied for all subjects, it is unlikely to make a big difference for the VBM analysis in the end. For the CSF compartment in which low prob values and low modulated values sometimes extend far beyond intracranial area, it can make a big difference (even for SPM5 based CSF maps), again arguing for thresholding, or alternatively, masking out extracranial values by a customised ot thresholded wholebrain mask. To get a feeling for the effect of thresholding it may be worth to try some thresholds and see what it does to "real" absolute mL of the total intracranial brain volume and the brain parenchyma fraction for which values have been published (well, if you have lots of time and want to make it perfect...) best regards, Philipp Max Planck Institute of Psychiatry NMR Research Group Kraepelinsr. 2-10 80804 Munich Mail: [log in to unmask] Phone: 0049-89-30622-413