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Dear Stephen:

Let me confirm. If the BET results with -R option is good for me, do you mean to add an extra flag -m to transform the BET result into a mask which can be used further to mask my 4D data?

Great thanks to your time.

Best,

Wei-Ta 


2013/4/16 Stephen Smith <[log in to unmask]>
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  


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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
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---------------------------------------------------------------------------
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
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