Jesper, many thanks!
Just a side question, I am wondering if you could recommend a brain label atlas (that is in MNI152 space).  My subjects have lesions in white matter (although not appear on T1, but appear on FLAIR, I can register FLAIR to T1 by flirt), so I want to use this label atlas to help compute the lesion volume in some white matter regions.  I do not want very detailed white matter atlas, an atlas that can divide the brain into a few regions  will be okay.

Best,
Ping

> Date: Mon, 26 Jan 2009 08:25:55 +0000
> From: [log in to unmask]
> Subject: Re: [FSL] template for fnirt
> To: [log in to unmask]
>
> Dear Ping,
>
> > So if I want to set --inwarp I have to edit the config file? can I add
> > --inwarp in the command line?
>
> It will be easiest if you simply add it to the command line, since you
> will need to specify a different set of warps for each subject.
>
> > Suppose I get my final template and begin to normalize the subjects to
> > this template, should I use the default config file with --ref=[my
> > template], all others are the same as the first time of iteration (during
> > creating t he model)?
>
> Once the template has been created, all the subjects that went into
> building the template will already be registered to the template. For
> "new" elderly subjects that you collect you will do as you describe above.
>
> Good luck Jesper

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