FSLers,
In case you find this useful, I am attaching my modified version
of the bourne shell sienax script that now allows one to pass
optional arguments to pairreg's call to flirt. an overview of the
differences:
% diff sienax $FSLDIR/bin
77d76
< echo "-F \"flirtopts\" : options to pass to pairreg/flirt (inside double-quotes), e.g. -F \"-
searchrx -20 20\""
111d109
< flirtopts=""
130,132d127
< elif [ $1 = -F ] ; then
< flirtopts=$2
< shift 2
174c169
< ${FSLDIR}/bin/pairreg ${FSLDIR}/etc/standard/avg152T1_brain ${I}_brain ${FSLDIR}/etc/
standard/avg152T1_skull ${I}_brain_skull ${I}2std.mat $flirtopts >> ${I}.sienax 2>&1
---
> ${FSLDIR}/bin/pairreg ${FSLDIR}/etc/standard/avg152T1_brain ${I}_brain ${FSLDIR}/etc/
standard/avg152T1_skull ${I}_brain_skull ${I}2std.mat >> ${I}.sienax 2>&1
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