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
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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Alison, Thank you very much for your advice. At least I know where the problem is, even though it doesn't look like I can solve it at the moment, since I have no writing rights to the file and our administrator is ... guess where? away in Boston, at Freesurfer and your home :) Hopefully I'll be able to fix it when he's back early next week. Will let you know
Many thanks again, Iwo
________________________________ 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
freesurfer@nmr.mgh.harvard.edu
-
Allison Stevens -
Iwo Bohr -
Pedro Paulo de Magalhães Oliveira Junior