Re: BET settings - ynic-users

13 Sep 2010

the -c option flag too can be useful and has virtually no cost .. this 
simple sets the centre of gravity to which the initial sphere is fitted. 
  find the coordinates of the AC in your participant (slice numbers) set 
the -c flag to this and usually the initial extraction is vastly improved.

Andre'

Chris Racey wrote:
...
  Thanks Tony,

 That's a good point, I will be in a position to do this comparison in the
 next day or so, after the analysis I'm running finishes. 

 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. 

 I will investigate the results of these procedures on statistical outcomes
 and post a comparison in the next couple of days.

 Chris

 -----Original Message-----
 From: ynic-users-bounces(a)ynic.york.ac.uk
 [mailto:ynic-users-bounces@ynic.york.ac.uk] On Behalf Of
 am501(a)psych.york.ac.uk
 Sent: 13 September 2010 17:43
 To: Chris Racey
 Cc: ynic-users(a)ynic.york.ac.uk
 Subject: Re: BET settings

 Thanks for this Chris.  Have you any side by side fMRI analysis with and
 without the -B option?  Ti would be interesting to see whether or the
 results of statistical treatments change and in what way.

 Tony

  Hi all,

 I was having some problems bet extracting some of my structural scans, I
 was
 getting a lot of left over neck that was screwing up the alignment. I
 noticed the current version of bet has a new option flag (to me at least),
 which focuses on cleaning up the neck.

 The option is -B . When using this flag the processing takes considerably
 longer, something along the lines of 10-15 mins per scan. However, not
 only
 did it resolve the issue, but the resulting image looks cleaner and more
 precise than I would expect from a normal bet. I've attached a comparison
 image so you can see the effect.

 I did similar comparisons running this flag with functional data and it
 also
 shows improvements. At the moment I'm re-processing my data files in this
 way before running my analysis.

 I thought I'd mention this in case it might be a useful option for other
 people to use, but also in case anyone knows any reason why it might be
 problematic. I'd be keen to know if anyone knows of any reason why I
 shouldn't use it? I notice the overall intensity seems slightly lower when
 this flag has been used, is this likely to be a problem?

 Cheers,

 Chris Racey

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Andre'

************************************************************************

Andre Gouws
York Neuroimaging Centre
The Biocentre
York Science Park
Heslington
YO10 5DG

Tel: +44 (0) 1904 435327
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