Re: BET settings - ynic-users

13 Sep 2010

On Mon, 13, Sep, 2010 at 05:53:51PM +0100, Chris Racey spoke thus..
...
  Actually, after my last message, Padraig came to see
me and mentioned
 another option -R which iteratively repeats the BET procedure from different
 starting points. He suggested that this may achieve the same improved
 result. I tried this option instead and indeed it does still seem to be an
 improvement. However it runs considerably quicker and doesn't seem to result
 in intensity changes in the image.  
That was going to be my suggestion too.  I don't now normally run bet
without using the -R flag.  As Andre says, changing the starting co-ords
can also help - for the record, the standard automatic cleanup for the
structural scans currently uses -c 90 116 166 but doesn't use -R.  I'm
not entirely sure why it doesn't as I thought it did (and was about to
say it did until I double checked).

I'll probably change this to use -R by default (for the automatic ones)
unless someone can remind me why it doesn't...

Mark

-- 
Mark Hymers
York Neuroimaging Centre