Dear Steve et al,
I am currently running FAST on a T1 MRI volume, before running BET, just to
get the RF bias field calculation and the corrected volume. The command
looks like this:
fast -t 1 -c 3 -or -n "$img"
This works OK, but it also takes a while to do the segmentation as well,
even though the -n option avoids output of the results.
I suspect that this is not the easiest/quickest way to get just the bias
field corrected volume?
The motivation here is to run BET on the bias field corrected volume,
assuming this should produce better results. Is it necessary to do this
before running BET, ie, does BET correct for RF biases internally?
Part of the motivation for this comes from the FreeSurfer processing
heirarchy. It normalizes first before extracting the brain. I'm no expert
on RF biases and intensity normalization, but I guess the FSL RF bias
calculation/correction is a different process from the FreeSurfer intensity
normalization. Any comments appreciated.
Cheers, Darren
--
Darren Weber, PhD Student
Cognitive Neuroscience, School of Psychology
Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
Ph: (61 8) 8201 3889, Fax: (61 8) 8201 3877
http://203.3.164.46/~dlw/homepages/index.html
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