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Hi - yes, unfortunately the reason this isn't practical is that almost no-one is writing information into the NIFTI header yet that would allow you to know where the top of the head or the nose is.....maybe in the future once this is more common.... Cheers. On 25 Mar 2009, at 15:47, Rolf Heckemann wrote: > The usage says > > -g <g> vertical gradient in fractional intensity threshold (-1- > >1); default=0; positive values give larger brain outline at bottom, > smaller at top > > I would have expected "bottom" and "top" to refer to the real world. > I still think that referring to a direction given by the data ordering > rather than the NIfTI header is a bug. > > > On Wed, Mar 25, 2009 at 03:19:07PM +0000, Steve Smith wrote: >> Hi - yes, the -g option refers to a vertical gradient on the -f >> option >> - if you want any other gradient you will need to reorient your image >> first. >> The usage lines says this ;-) >> Cheers. >> >> >> >> On 25 Mar 2009, at 14:24, Rolf Heckemann wrote: >> >>> I am getting different results from BET depending on the data >>> ordering >>> in the NIfTI file. It appears that BET relies on the data >>> ordering to >>> determine the vertical axis in the image. I would expect BET >>> results >>> to be identical on pairs of files that only differ by the data >>> ordering. >>> >>> I've illustrated the problem on this page: >>> >>> http://www.soundray.org/betbugdemo >>> >>> >>> -- >>> Rolf A Heckemann, PhD >>> Research Associate >>> Division of Neuroscience and Mental Health >>> MRC Clinical Sciences Centre >>> Imperial College London >>> Hammersmith Hospital Campus >>> Du Cane Road >>> London W12 0HS >>> United Kingdom >>> 1237990828 >>> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> --------------------------------------------------------------------------- > > -- > Rolf A Heckemann, PhD > Research Associate > Division of Neuroscience and Mental Health > MRC Clinical Sciences Centre > Imperial College London > Hammersmith Hospital Campus > Du Cane Road > London W12 0HS > United Kingdom > 1237995727 > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------