Hi,
A colleague is trying to run FIRST and has run into a problem with
first_flirt producing incorrect standard space registrations (for
example 90 degree rotations in the sagittal plane with a resulting match
to the wrong part of the head. Starting with brain extracted images is
more successful, but we've noticed the warning on the FIRST page
"Although it is generally discouraged, the flag *-b* will allow
*|first_flirt|* to also be used on brain extracted data."
However I've checked the FMRIB technical report and Brian Patenaude's
thesis and haven't been able to find out why it's discouraged; is it
simply to avoid using the BETed images further down the pipeline or a
concern about the registration that would result? I ask because one
solution that's been suggested is to use the brain mask from BET as an
input to -inweight, which should produce similar results for the
registration, but without masking out non-brain tissue in the resulting
image.
Thanks for your time,
Ian Malone
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