Ed,

Create a file (named whatever you want, say, mri_nu_correct.xopts) containing one line:

mri_nu_correct.mni --distance 25 --stop 0.0001 --fwhm 0.1

and then include this at the end of your recon-all command:

-expert <pathto>/mri_nu_correct.xopts

and it will append those three flags to the end of the nu_correct command.

Nick

On Tue, 2009-04-28 at 16:05 +0200, Ed Gronenschild wrote:

Hi,

I want to use parameters different from default for mri_nu_correct.mni. This command uses nu_correct for which I would like to set the following options:

-distance 25 -stop 0.0001 -fwhm 0.1

These settings are more approriate when using 3T T1 data. How can I invoke these in recon-all? Can I use an options file?

Ed

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