If you want to just run the recon-all pipeline without using n3, you'll have to do something else. You can copy orig.mgz to nu.mgz (or create a symbolic link, which is probably better), then run with -nonuintensitycor

On 1/29/18 7:14 PM, Alexis Moscoso wrote:

Hello Freesurfer developers,

I’m trying to run a recon-all on ADNI T1 images. Since these data have already been corrected with the N3 correction, I want to turn off N3 correction in the recon-all process so I added -nonuintensitycor after -all. However, when I run it, I get an error during the normalization step since it no nu.mgz file is generated and cannot be found by mri_normalize. I’d like to know how to do the everything except the N3 correction.

1) Freesurfer version: 6.0.0

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