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Hello, I have a set of phase images (a time-series of one single slice) which I want to register. So I flirted the corresponding magnitude images to the reference image (which is the first image of the time series) and applied the same transformation to the phase images. While the transformation works nicely for the magnitude images, applying the same matrices to the phase creates blank images I did the following: /usr/local/fsl/bin/flirt -in ../magnitude.nii -ref ../magnitude.nii -out ../reference_magnitude.nii -omat ../new_magnitude.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -2D -dof 12 -interp trilinear /usr/local/fsl/bin/flirt -in ../phase.nii -ref ../reference_magnitude.nii -out ../new_magnitude_shadowreg_phase -applyxfm -init /mnt/hgfs/FSLshared/new_magnitude.mat -interp trilinear Help would be much appreciated. Best regards Jakob -- Dipl. Phys. Jakob Bindl Universität Bonn Helmholtz-Institut für Strahlen- und Kernphysik Arbeitsgruppe Maier/Urbach Raum 0.011 Nussallee 14-16 D-53115 Bonn Tel: +49 (0) 228 73 3893 Fax: +49 (0) 228 73 2505 E-Mail: [log in to unmask] www.mrt.uni-bonn.de