Does anyone have any tips on using BET to skull strip T1 weighted scans in
very young children (under 6 months)?
I have been adjusting the intensity settings and got a reasonable result
with -R -f 0.7, but there is a persistent small patch of skull remaining in
the occipital region of every child under 6 months. I would like to improve
on this, as it messes up any co-registration I then go on to do (I also
would like to get measurements for brain volume).
Are there any other settings that people have found useful to tweak in this
situation?
I am also having trouble getting a satisfactory brain extraction on some
other scans with more severe abnormalities - is there any way to mask out a
region so that it is ignored by BET? (A couple of the children have had
previous neurosurgery for VP shunt insertion and the edges of the surgical
lesion are not dealt with very well by BET.
Many thanks,
Michael
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