Iwo,
If you do
ls $FREESURFER_HOME/bin
Do you see mri_nu_correct.mni there?
If you do, this message might help you:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
Essentially, you have to make sure the nu_correct uses perl so you need to
make sure it knows where it's located.
If you don't have that binary, then you'll need to download it.
Let us know,
Allison
--
On Fri, 29 May 2009, Iwo Bohr wrote:
Hello everybody,
Since I was corresponding with a few persons separetly, it required resending
the same information to all of them.
So I am getting back to the general forum with my still unsolved problem.
To recap: when I run recaon-all pipeline as below:
[iwob...@huxley FMRI]$ 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
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