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Hi Yes, this is possible with flirt. You'd use the -applyxfm -init options which allow you to specify an affine transformation matrix (as a text file), and that matrix would specify your rotation. No different to applying a transformation to an image, only in that in this case you'll need to build the transformation matrix yourself. The transformation matrix may take the form: [[R] 0 0 0 0 1] with R a 3x3 Cartesian rotation matrix. Easy in Matlab/Python/Octave etc (Matlab has the rotation matrices in the aerospace toolbox). You might also want to centre your images on the origin of the coordinate system first. Michael Knight Elizabeth Blackwell Institute early career fellow University of Bristol On Thursday, 10 December 2015, Yang, Daniel <[log in to unmask]> wrote: > Dear FSL experts, > > Is it possible to manually rotate a NIfTI file to a particular degree in > the X, Y, or Z dim in a 3D space? > > Many thanks!! > Daniel >