I am planning an analysis using freesurfer to compare 2 groups. The SPGRs that will be used vary in regard to slice thickness (from 0.86 to 1.5 in each axis), number of slices acquired (100-256), and orientation (axial; coronal) due to the fact that these were collected over a number of years on the same scanner. In another posting I read that this might be a problem but wanted to revisit this to see if any specific heterogeneity in the parameters should be particularly avoided. Also, if the groups differ such that one group has largely similar scan parameters and the second group is more heterogeneous, will this introduce any systematic bias in cortical thickness estimates, parcellation, or segmentation values? Thanks for any advice on this issue.