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I'm not sure exactly what AFNI's 3x4 matrix represents, but you probably just need to change the header information for SPM to be happy with the files. Note that I would suggest only applying a rigid-body transform to the headers (using spm_get_space), so the extra stuff (zooms and shears) should be factored out from the affine transform. If you apply a full affine transform, then any volumetric measurements will be a bit off and it is likely that the registration procedures in SPM will be sub-optimal (because it "knows", a priori, roughly how much to zoom a typical head to match it to the MNI data). Best regards, -John On Friday 11 July 2008 20:13, Michael Yassa wrote: > Dear SPMers, > > I would like to use John's reorient.m script to do change the orientation > of images. I acquire brains in a tilted oblique orientation and would like > to use AFNI to automatically get them approximately in talairach space. > AFNI outputs the parameters it uses as a 3x4 matrix of translations, > rotations and scales (the same params that can be specified using Reorient > images in the GUI). > > I would like to use reorient.m to apply these parameters and create a new > mat file (or adjust the old one) without interpolating and writing new > files. I'm not sure which of the params in reorient.m would allow me to do > this. If it's not possible, is there a command line version or function for > reorient images that I can modify for this purpose? The idea is to create a > mat file that can then be combined with DARTEL transformations so I would > only have to interpolate once. > > Thanks so much. > > Best, > > Mike Yassa