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From: Allison Stevens <astevens@nmr.mgh.harvard.edu>
To: Iwo Bohr <iwobohr@yahoo.co.uk>
Cc: Freesurfer@nmr.mgh.harvard.edu
Sent: Friday, 29 May, 2009 13:58:54
Subject: Re: [Freesurfer] brainmask.mgz recan-all and nu_correct error

Iwo,
If you do
ls $FREESURFER_HOME/bin

Do you see mri_nu_correct.mni there?

If you do, this message might help you:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html

Essentially, you have to make sure the nu_correct uses perl so you need to
make sure it knows where it's located.

If you don't have that binary, then you'll need to download it.
Let us know,
Allison

--

On Fri, 29 May 2009, Iwo Bohr wrote:

> Hello everybody,
>
> Since I was corresponding with a few persons separetly, it required resending the same information to all of them.
> So I am getting back to the general forum with my still unsolved problem.
> To recap: when I run recaon-all pipeline as below:
>
> [iwobohr@huxley FMRI]$ recon-all -autorecon1 -i NCVI-JR001TH_T1WIR_brain-conv.nii.gz
>   -subjid test -all -force
>
> (with -autorecon1 option or without, similar situation occurs with -make option)
>
> It fails to output many necessary files, including brainmask.mgz, and the error message upon the completion of the pipeline is as follows:
>
> ERROR: nu_correct
> recon-all exited with ERRORS at Thu May 28 12:06:45 BST 2009
>  
> I attach a more detailed log file.
> I hope that now somebody will be able to help me :)
>
> Many thanks in advance,
> Iwo
>
>
>