13 Sep
2010
13 Sep
'10
4:53 p.m.
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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