Hi - no, this isn't necessary - you can just use the -F option to
process 4D FMRI data with BET - no need to split up the data.
Cheers.
On 29 May 2009, at 22:03, Andrew Jahn wrote:
> Hi,
>
> I recently ran the following set of commands on a series of EPI images
> (run1, run2...run6) in order to remove some noise and other artifacts
> outside of the brain (e.g., eyes):
>
> ================
> #!/bin/bash
>
> mkdir run1
> mkdir run2
> mkdir run3
> mkdir run4
> mkdir run5
> mkdir run6
>
> mv s001.nii run1/
> mv s002.nii run2/
> mv s003.nii run3/
> mv s004.nii run4/
> mv s005.nii run5/
> mv s006.nii run6/
>
> for f in run*; do
> cd $f
> fslsplit *nii
> cd ..
> done
>
> for f in run*; do
> cd $f
> fslsplit *nii
> cd ..
> done
>
> for f in run*; do
> cd $f
> for ff in vol*; do
> bet2 $ff b${ff}
> done
> cd ..
> done
>
> fslmerge -t imageAfter bvol*
>
> =================
>
>
> Is this an appropriate use of bet2, or is it essentially doing the
> same
> thing as a mask at a later preprocessing stage? One reservation I
> have is
> that the process appeared to artificially inflate the image
> intensity. Any
> input is appreciated.
>
> Thank you,
>
> -Andrew
>
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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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