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Hi, Could you let us know the exact commands you are using and upload your data to: https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C so that we can look into what is going wrong. All the best, Mark On 25 Jan 2014, at 15:03, Ray Lee <[log in to unmask]> wrote: > Just wondering what is the difference in handling nifti header between atlasquery and fslview? I have a rotated data set. After using "fslreorient2std", it's turned to MNI standard orientation with right-handed coordinate (all diagonal terms in sform and qform matrix are positive). In fslview, the right side activation is located in the side labeled as "R", which is correct, but "atlasquery" results shows that activation is on the left side. > > I used "fslorient" to reset the matrices so that the coordinate is turned to left-handed which is the original MNI standard coordinate, but the activation region in fslview now is flipped to the left side, and the atlasquery still shows left activation. Now both are wrong. > > Any suggestion on a quick fix for this. > > Thanks in advance. > > Ray