Jesper, thanks for your detailed explanation.  So when I do fnirt, I should use the 2mm template; after I get the nonlinear_transf, I can  still apply it on my T1 and set --ref to the MNI_1mm template, then I will get my warped subject in the 1mm space.  You can reply me if I mis-understand it.  Thanks again, Ping

> Date: Sat, 24 Jan 2009 17:40:40 +0000
> From: [log in to unmask]
> Subject: Re: [FSL] template for fnirt
> To: [log in to unmask]
>
> Dear Ping,
>
> > Great, I am going to try soon, I want to creat a 1mm template
> > (MNI152_elderly_T1_1mm), should be the same procedures as long as I use
> > MNI152_T1_1mm instead in the first step? Let me know if I understand
> > correctly.
>
> you could use the 1mm template throughout the procedure. However, the 1mm
> has unnecessarily high resolution given that with fnirt you will typically
> use a warp-resolution of no less than 6-8mm (10mm being the default).
> Therefore I would recommend using the 2mm MNI template to start things,
> and then keep the whole process at 2mm until your procedure has converged.
>
> Once it has converged, if you still want a 1mm template, you can use the
> last warp-field for each subject and run applywarp again, this time
> specifying the MNI152 1mm template as --ref. That means all your subjects
> will be warped into the same space as before (your elderly MNI space) but
> now on a 1mm grid. These can then be averaged to give you your 1mm
> template.
>
> Good luck Jesper

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