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This is exactly as expected. spm_read_vols expects all the voxels in the images to be aligned with each other so that voxel i,j,k in one image corresponds with the same piece of tissue as voxel i,j,k in another. However, the matrices in the .mat file say that the voxels should be displaced relative to each other and don't line up this way. If you reslice the images, then you should be able to use spm_read_vols on the resliced version. Same goes for the unwarped version. Best regards, -John On 1 November 2017 at 19:33, dead man < [log in to unmask]> wrote: > Dear SPM Users/Experts, > > After I have run any of the realignment modules (say realign and unwarp) > on fMRI 4D dataset, if I try and open the original functional volume in > MATLAB using spm_read_vols(spm_vol(filename)), I get an error stating > that the images do not all have same orientation and/or voxel sizes. The > error message displays the matrix for all the volumes and then mentions > that the orientations must be identical for this procedure. > > Is this expected? Do I understand this correctly that when we run > realignment, the headers are moved by some amount (which is a function of > the movement between the reference scan and the volume)? If so, does this > mean that my original functional data becomes sort of useless? The unwarped > version created after this step does not create this problem. > > > Thank you very much for your time! > > > With kind regards > Patrick > -- Prof John Ashburner Professor of Imaging Science UCL Institute of Neurology Queen Square Wellcome Trust Centre for Neuroimaging University College London 12 Queen Square, London, WC1N 3BG E: [log in to unmask] T: +44 (0)20 3448 4365 http://www.fil.ion.ucl.ac.uk/