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Hi I'm a little confused: your fullanalysis.txt file has a feat directory as input? Otherwise, the registration.txt file looks OK I think. It will overwrite the existing registration in the feat directory that you have provided as input. Is this what you were expecting? Eugene -- Centre for Functional MRI of the Brain (FMRIB) | University of Oxford John Radcliffe Hospital | Headington OX3 9DU | Oxford | UK Ph: +44 (0) 1865 222 523 | Mob: +44 (0) 7946 362 059 | Fax: +44 (0) 1865 222 717 -- On 11 April 2010 20:41, Paul Trowbridge <[log in to unmask]> wrote: > We are trying to run separate, partial feat analyses, i.e., prestats, > registration only, post-stats, etc. However from both a command-line run > file and via the fsl gui all inputs results in a full analysis run. We > think the only difference in the designs are the set fmri(analysis) and set > feat_files(1), there may be another setting required that we don't know > about. We have the input correct, the design.fsf read according to intended > analysis, however full analysis is performed. We are attaching design.fsf > files for a registration only and full analysis run. > > >