Thanks Pedro, I was just thinking about it. Iwo
________________________________ From: Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br To: Iwo Bohr iwobohr@yahoo.co.uk Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Friday, 29 May, 2009 14:26:01 Subject: Re: [Freesurfer] brainmask.mgz recan-all and nu_correct error
Iwo
To find where Perl is type: which perl
--- Pedro Paulo de M. Oliveira Junior
2009/5/29 Allison Stevens astevens@nmr.mgh.harvard.edu
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
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