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Hi, I have 3T epi data for which I don't have field maps and am trying to achieve the best registration possible by using an initial highres (6DOF to an epi obtained during rest) and the subject's structural T1 en route to the template. Mark has previously suggested to me that my best bet is to use cost function masking. I've tried following the tips provded by Matthew Brett on the CBU page, although these are designed for SPM. In tyring to extrapolate them for the purposes of FEAT analysis,a few issues have arisen: 1 - Would I have to mask just the initial highres, or both the initial highres and task epi? If the latter, would I just mask the middle volume, as this is what is used in the registration? If so, my 4D file contains 160 volumes. Would the middle correspond to the 79th, or the 80th? 2 - The CBU page recommends co-registering the epi to the structural and using the "yoke" function in MRIcro to identify points where there is signal dropout in the epi relative to the structural. These are the portions that should be masked out. If I register the unmasked epi to the structural, wouldn't this yield a (relatively) poor correspondance between the images, so that using this as the basis for identifying signal dropout would not be the best way to go about it? Are there any alternative ways for idetifying which areas to mask out? 3 - Following from 2, would there be any problems in doing a straight image subtraction to identify the areas to be masked? It seems to me that this would be plagued by the same problems as in 2, but that it would be a quicker way to go about it? 4 - The CBU page recommends smoothing the mask image (8mm in accordance with the SPM default). Would I also need to do this with FEAT? Would I use 5mm, as this is the FEAT default (or alternatively, whatever level I set it to)? 5 - As an aside, can someone tell me why the average epi template in SPM would be a poor choice as an intial highres? Does the fact that it's not the same brain as your subject introduce more problems than the advantage of having the added contrast? Sorry if some of these questions seem a bit basic - still trying to get my head around all of this! Thanks heaps, I really appreciate your ongoing help! Alex