try running: fixup_mni_paths
On Fri, 2009-06-19 at 09:38 +0200, Ahmed, F, Me wrote: > Sorry, according to the thread that you provided me, nu_correct uses perl, so > make sure that perl is found at: > > /usr/bin/perl > > > "perl" is found at /usr/bin/perl, so it is in the correct place and > theoretically, it should be working. But it isn't. Is there any reason why > that could be happening? > > Sorry for the constant questions. > > > -----Original Message----- > From: Sita Kakunoori [mailto:s...@nmr.mgh.harvard.edu] > Sent: 18 June 2009 18:29 > To: Ahmed, F, Me <fah...@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 <fah...@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:fis...@nmr.mgh.harvard.edu] > > Sent: 17 June 2009 17:12 > > To: Ahmed, F, Me <fah...@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 > > <fah...@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: > >> > >> [...@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 > >> > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
