Hi Ilana

that won't work. I guess you could try copying nu2.mgz to nu.mgz and
trying -make all (assuming you have a new enough version of recon-all)

cheers
Bruce
On

Tue, 4 May 2010, Ilana Hairston wrote:

> Also re-sending my query - perhaps someone has experience with contrast
> adjustments
>
>
>
> We have been doing contrast correction using mri_nu_correct.mni after
>> autorecon-all
>>
> (e.g.,
>>
> mri_nu_correct.mni --i FS090620ll/mri/orig/001.mgz --o
>> FS090620ll/mri/orig/nu2.mgz --n 2).
>>
>
>
>> My question is whether after doing subsequent edits and corrections (such
>> as adding control points, or editing white matter) do we need to specify
>> nu2.mgz as the target file for the recon fix steps in the command line
>>
> (e.g.,
>>
> recon-all -autorecon2-cp -autorecon3 -s FS090620ll -i
> FS090620ll/mri/orig/nu2.mgz
>> -force)
>>
>>
>
>> thanks
>> ilana
>>
>
>
>
>

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