After Tim Jarvis reported problems with SureFit omitting large parts of
cortex near the eye, we carried on further discussion off-list.
While some of you may have experienced cases where SureFit failed to
fully remove all the eye fat (requiring well-placed zaps in either the
segmentation or input volume), only a few cases I know has SureFit eaten
into cortex, mistaking it for eye fat. In Tim's case, his skull and eye
fat were already removed, so the misbehaving code wasn't even
applicable. If this happens to anyone else, shift-click this link and
save it into $SFHOME/lib/SureFit:
http://brainmap.wustl.edu/pub/donna/Scripts.py
login pub
password download
If all your input volumes will be stripped of eye and skull (e.g., run
through something like FSL's brain extraction tool), then insert this
line near the top of $SFHOME/bin/utility.sh:
export SUREFIT_SKIP_EYESTRIP="YES"
If only sometimes, you'll have to set the environment variable on the
command line before starting SureFit. For tcsh users, the command is a
bit different:
setenv SUREFIT_SKIP_EYESTRIP "YES"
When we move SureFit into Caret, we'll make this easier to configure.
