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> 1) When doing Realignment (Estimate & Reslice), it is standard to select Wrapping: No wrap. Is this correct? There is not really such a thing as "standard" in science, as this would prevent us from gaining new knowledge. Most people would not use wrapping though, but it can be useful for data where the head positioning was not so good (and the face pokes into the back of the image etc). > 2) Is the following sequence standard for the indirect preprocessing method? > Coregister (Estimate) > Segment > Normalise (Write) This is what most people currently use. > > > 3) Within Normalise (Write) Writing Options, you must state the Voxel Sizes. Our acquisition voxel sizes are: 1.7 x 1.7 x 3. Would we then state 3 3 3 for the Voxel Size? Smaller voxel sizes are theoretically better (because the random field assumptions are best satisfied), but if the voxels are too small, then you quickly run out of disk space. Generally, I would suggest using the default settings of 2mm isotropic, which is what most people would do. > > 4) Under Smooth, you must select the kernel size: "Highlight FWHM." We recall that many people double the voxel size. Therefore, if it is 3 as stated above, would we then choose 6 6 6 here? The optimal smoothing will depend on the size of the blobs you expect to find, the accuracy with which data can be aligned across subject, and various other factors. Random field theory is most accurate when the FWHM is a few times greater than the voxel sizes. More smoothing also means you have fewer independent tests, so statistics based on peak height will have fewer multiple comparisons to make (so smaller corrected p values). On the negative side, you can not be so specific about where the differences actually are. I could be wrong, but think most people currently use in the region of 8-12 mm FWHM of smoothing. Best regards, -John