Dear BettyAnn,
The search restrictions should be adhered to in the pairreg
schedule files, and almost all other schedule files. In fact,
the normal flirt run effectively uses an internal, default
schedule file so this is nothing unusual. Only schedule
files that do not perform rotational searches will ignore
these search parameters.
All the best,
Mark
On 27 Jun 2007, at 03:24, Bettyann Chodkowski wrote:
> Hello All,
>
> I just modified sienax to pass additional flirt options to pairregs:
>
> flirtopts='-searchrx -15 15 -searchry -15 15 -searchrz -15 15'
> ${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
>
> But I now see that pairregs uses -schedule. Will the rotational
> search restrictions be incorporated in with the -schedule
> parameters? (I am running a test right now ....)
>
> If not, can the -schedule file be modified to restrict the search?
>
> Thank you,
> - BettyAnn
