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Hi Mark so I think we have solved it. It was multi-factorial. A combination I believe of permission corruptions but also an odd file sitting in the user's .qt directory We found .qt/fslrc with these contents atlaspath=/usr/local/fsl/5.0.1/data/atlases^e fsldir=/usr/local/fsl/5.0 mni=/usr/local/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz 1. What writes this ? Not all users I looked at had the fslrc file. Many had other harmless files. 2. It's bad that the full atlas path has been translated (as when installations change the root e.g. /usr/local/fsl/5.0 does not change as it's symlinked to the current actual install e.g. /usr/local/fsl/5.0.1 That ^e on the end of the first line looks interesting... regards Neil