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Hi - get a 3D bet brain mask that you like and then mask the 4D data with it using fslmaths fslmaths my4d -mas my3d_bet_mask my4d_masked Steve. On 16 Apr 2013, at 15:18, Wei-Ta Chen <[log in to unmask]> wrote: > 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 > --------------------------------------------------------------------------- > > > > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------