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Update: I rotated the functional images about the y axis using rri_orient (http://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image) Doing so, the nii file header shows the rotated files to have the dimensions: 4 64 64 40 121 1 1 1 The original files had dimensions: 4 40 64 64 121 1 1 1 Unfortunately, this did not seem to solve my problem, though I am in the process of determining how an intervening step (expanding the 4D volumes into multiple 3D volumes) undid the rotation, as the expanded files have the dimensions 3 40 64 64 1 1 1 1 In any case, simply rotating the 4D files is not a quick fix.