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Dear Stephen: One more question. After skull stripping by BET, I usually extract the 7th volume of my resting-state recordings (200 time points in total) by fslroi for further linear and nonlinear registration. However, using both flags (-R and -F) of BET, I cannot extract one specific volume by fslroi. Previously I used only -F flag of BET and fslroi worked. Why? It seemed "bet <input data> -F -R" yielded a "concatenated" single volume rather than a time series with separate volumes, as I checked the BET results by fslview. Should I use the flag -f instead and find tune the f value to get the best BET results (for the sake of fslroi use) ? Best, Edward 2013/4/16 Stephen Smith <[log in to unmask]> > Hi - no, presumably all that has changed is the auto-setting of the > intensity display range in FSLView - this is fine. > Cheers. > > > On 16 Apr 2013, at 04:34, Wei-Ta Chen <[log in to unmask]> wrote: > > Dear FSL experts: > > I used BET with the flag -F to strip skulls of my resting-state fMRI > recording. However, there remains some skull layer outside the brain. When > I used BET with the flags -F and -R, the results was much better > without remaining unwanted skull layers. > However, I found the brain extracted skull by the former method (using > single flag -F) looked "brighter" under fslview compared to that extracted > skull by the latter method (using flags -R and -F), although the > voxel-specific intensity value read the same by both methods. > > Will this difference influence my later processing of resting-state data? > Any suggestion? Thanks. > > Best, > > Edward Chen > Taipei Veterans General Hospital > > > > --------------------------------------------------------------------------- > 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 > --------------------------------------------------------------------------- > > > >