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John, Thanks for your reply, it seems to be exactly what I'm looking for. I'm having diffuculties though using either this or what Michael suggested (probably because of my lack of experience with analyse/nii and SPM in general... When I use normalization I get a warped version of my source image which is in good alignment with the reference (I checked that with spm_check_registration(images)) However, the output matrix size is not the same size as the reference (and that's why I can't use Michael's approach) When I use the deformation tool (using a parameters file saved in a normalization process) I get 3 3D matrices, the same size as the reference, but I'm having troubles interperating the results... So any suggestions to what I'm doing wrong will be very much appreciated Thanks again, Yonatan On Mon, Jun 6, 2011 at 10:24 AM, John Ashburner <[log in to unmask]> wrote: > You could try the Deformations utility. This will write out a y_* > image (containing three volumes, [:,:,1,1], [:,:,1,2] and [:,:,1,3]) > that encodes the mapping. You'll need to account for voxel-to-world > transforms in image headers to make use of it though, as the mapping > is saved in mm coordinates. The code is in spm_defs.m. > > Best regards, > -John > > On 5 June 2011 05:49, Yonatan Dinai <[log in to unmask]> wrote: >> Hello all, >> >> I've used the "normalize" function of SPM, and was able to warp two >> volumes succesfully. >> >> I would now like to use the output parameters of the normalization >> process - the 4x4 matrix of the affine transformation & the 4D matrix >> of the DCT coefficients to transform an input point (X,Y,Z in the >> source volume) into it's mapped point in the reference coordinates? >> >> Does anybody has a code the computes that transformation? Is there >> such a function on SPM? If not, I would be happy to hear of any fast >> way to compute such a transformation. >> >> Thanks a lot, >> >> Yonatan >> >