Hi,
Thank you for your help and in providing that link. I found "perl" and set it to the correct place, tried to do "fixup_mni_paths", and got the following message when trying to find "nu_correct"
[fsl@localhost bin]$ nu_correct Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.7/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.7/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.8/i386-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /home/fsl/Desktop/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /home/fsl/Desktop/freesurfer/mni/bin/nu_correct line 37.
This all seems very confusing and I'm not sure what is going on. Everything seems to be in place in order for freesurfer to find "nu_correct" but it's just not working. Please help!
Thank you. Fatima
-----Original Message----- From: Sita Kakunoori [mailto:sita@nmr.mgh.harvard.edu] Sent: 18 June 2009 18:29 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] error message
're-run with force' means that the subject name exists and using the 'force' flag will overwrite it. As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
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