Dear Brittany,
> I am trying to make a study-specific template using T1 images of
> rhesus
> monkeys. I am new to FNIRT and was wondering if anyone had a set of
> parameters that I could start with. Thanks
the best point to start would be with the T1_2_MNI152_2mm.cnf
configuration file, and then change the appropriate parameters. There
are quite extensive explanations of the various parameters at http://www.fmrib.ox.ac.uk/fsl/fnirt/index.html
The parameters that you are likely to need to change are
--subsamp, --warpres
You should note though that this configuration file is for a single
scanA->scanB registration case, and that in order to build a template
you would need to write a script that first generates an initial
template (typically the average of all the scans after registering
them to an arbitrary sample within the population) and then gradually
refine that template by iteratively re-register all the scans to the
template.
I really ought to write a little "template making" script, but I am
afraid it will not happen in the next few weeks at least.
Good luck Jesper
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