Dear Joel,
>
> I would like to register a patient's FLAIR data with that same patient's FA data.
> Is this possible and if so, is there a standard way to do this ? (i.e. do I use FLIRT or FNIRT?
when registering within-subject-between-modailty we generally recommend FLIRT.
> What cost function do I use?
For FLAIR to FA I think mutualinfo or normmi are your best bets. You should also BET your flair images first.
> Do I use cost weighting for white matter hyperintensities in the FLAIR data?
If these are small and localised I suspect it won’t make a big difference. Though it can of course never do any harm to.
> Do I use the FA configuration file for FNIRT?)
Always use a config file with FNIRT, but not in this case since you are using FLIRT.
Jesper
> Thanks in advance.
>
> Kind regards,
> Joep Kamps
>
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