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Hi. > This way the mask ends up to slices 13-16 of the epi-image. > As I have the T1 axial volume taken with the same slice > prescription as epi I know the area of interest is in slices 10-13. Also > judging on the basis of the form of the lateral ventricles one can see > that the transformed mask lies too high. > > This is not a great problem any more since I have found one way around it > but not being able to use the initial highres according to my original > plan bugges me. You might be better off taking the functional into the space of the highres. Probably there is some slight mismatch between the images, and it's generally better to work in whichever space has the higher resolution. > > Ah, no, I'm saying that the voxel sizes in one or other of the original > > images was slightly _wrong_, not that they should be set to be the same! > > Ie the true voxel size in one or other image was not exactly what was put > > into the header. You will need to use greater than 3DOF to find out what > > the right ratio of voxel sizes should be. > > Really - how can that be found out? I think that if there is a discrepancy > with true voxel sixe and the size announced in the header this might need > some scrutinizing. Also, if one can find out the "amount" of discrepancy > could one scale the initial highres with a factor which could correct it? if you use avscale matrixfile input_volume you'll get a breakdown of the transformation matrix. Cheers, Steve. Stephen M. Smith DPhil Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve