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Hi, I posted this before on 4 July and recently on 24 August. We are experiencing serious problems with TBSS. A close inspection of the 4D stack all_FA.nii.gz in the stats folder revealed that more than 80 % (!!!!) of the FA maps were badly registered to the default FA template FMRIB58_FA_1mm (we used the -T option in tbss_2_reg). It turned out that these problems got resolved by flipping the y coordinate of the offending FA maps beforehand (using fslswapdim), although these were correctly oriented (as shown by fslview). Our conclusion is that by some unknown reason the registration tool fsl_reg spontaneously introduces a y flip of the data in the majority of the cases. These problems persisted in three different projects, two of which based on a Siemens MRI scanner and one based on a Philips scanner. We used FSL version 4.1.4. Ed