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Hi - The TBSS framework is more or less independent of the method you use to calculate FA. You can calculate FA using the free water elimination method and then feed the results to TBSS. I am not sure, though, what software package has this method implemented (see Pasternak 2009). Cheers Saad On 18 Feb 2013, at 17:21, Judit Haász wrote: > Dear FSL developers, > > recent papers discussed the importance of correcting for CSF contamination, WM atrophy in DW-MRI analysis based on Pasternak et al in MRM, 2009. > are there any possibilities that FWE will be included in the TBSS pipeline in the near future? > > Best regards > Judit Haasz -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad