Dear Mark,
Yes, indeed. This is interesting to know. And, in fact,
my empirical test confirms what you explain (not that
I doubted you :) The rotational search restriction was
honored in addition to the -schedule.
Thank you and regards,
- BettyAnn
On Wed, 27 Jun 2007 08:32:52 +0100, Mark Jenkinson <[log in to unmask]> wrote:
>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
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