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Hi - it's probably simpler than you're imagining - actual registrations are only run for each incremental pair of images, namely your steps 1,2,3,4 are actual registrations, and are all displayed on the report page. Any other transforms (eg 5) are created by mathematical concatenation of matrices and don't need any further checking if 1-4 look ok. For any given transform, if you don't have a saved image that you want to evaluate, you can take an input image, a reference image, and apply a saved transform with FLIRT without re-estimating the transform, using -applyxfm -init <transform> Cheers. On Fri, 17 Sep 2004, Alex Fornito wrote: > Hi, > I'm registering me task EPI via a wholehead EPI (6 DOF), the person's > structural (7 DOF), and then to the template (12 DOF). The FEAT report > gives visual overlays for 4 registrations: > 1- task EPI to wholehead EPI > 2- wholehead EPI to highres structural > 3- task EPI to highres structural > 4- highres structural to template > 5- task epi to template > > I understand the rationale for registering the task epi to the highres > structural via the wholehead epi, and the then to the template via the > highres structural, but could you please explain the steps, and what > happens (e.g., which transformation matrices get applied to what and > why?). I've had a bit of trouble working it out from the scripts in > the .log file. > Also, I've noticed FEAT spits out the .mat files, but is it possible to > extract the registered images, so that I can overlay them (as per the 5 > images above) in medx and check the registration in more detail? > Appreciate your help, > Alex > -- 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