Hi Zeke,

Thanks so much for your prompt response. My PATH variable is /usr/global/freesurfer/5.3.0/freesurfer. I do see nu_correct in the /usr/global/freesurfer/5.3.0/freesurfer/mni/bin, so that seems to be correct as well.

Should I export my PATH environment variable to include /mni/bin?

Thanks again, Natalie

On Mon, Oct 28, 2013 at 12:23 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:

Hello Natalie,

'nu_correct' should be found in your '$FREESURFER_HOME/mni/bin' directory. That directory should be added to your PATH when your source the SetUpFreeSurfer.sh file. You can probably get around this issue by adding $FREESURFER_HOME/mni/bin to your PATH environment variable. But Im curious why its not there to begin with, and what does your PATH variable look like after you source the SetUpFreeSurfer.sh file.

You can display it using the following command: echo $FREESURFER_HOME

-Zeke

On 10/25/2013 04:09 PM, Natalie Garcia wrote:

...

Hi all,

I've tried running auto-recon with version 5.3.0 (on Mac OSX v10.8.2) and the processing stream seems to fail at the intensity correction point. Not sure if it helps, but when I look at the output from the PBS script, I see "nu_correct: Command not found."

Any suggestions on what I might be able to do to fix this? Any help would be greatly appreciated.

Natalie

-- Natalie V. Garcia Graduate Student, Cognitive Psychology Psychology Department The Pennsylvania State University 423 Moore Building nvg109@psu.edu mailto:nvg109@psu.edu

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