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In the standard Analyze format, there is no space allocated in the headers for the orientation of the images. This is why additional .mat files are used by SPM99 and SPM2. If the converter doesn't create such .mat files, then the direction cosines will simply be the default values. One of the features of NIFTI is that space in the headers has been used in order to store the orientations of the images. Best regards, -John > I am converting to both Analyze and Nifti format with the freesurfer > tool mri_convert (from COR format). > > When I convert to Analyze and display in SPM5b, the head is flipped > around in a funny way and the dir cos matrix is identity. > > When I convert to Nifti and display in SPM5b, the head is in what > seems to be correct orientation with dir cos [1 0 0 ; 0 0 1 ; 0 -1 0]. > > When I display Analyze format in SPM2, it looks like the Nifti > display of SPM5b and the dir cos is also [1 0 0 ; 0 0 1; 0 -1 0]. > > Are the dir cos just a function of display? Should I be worried > about this?