Sorry. I mistyped the first command (Wrong) recon-all -i DICOM_FILE_DIR -o 001.mgz
(Correct) mri_convert -i DICOM_FILE_DIR -o 001.mgz ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br 2009/6/17 Ahmed, F, Me <fah...@sun.ac.za> <fah...@sun.ac.za> > PPJ, > > > > Thank you for your response, I tried your procedure and got the following > message: > > > > [...@localhost CON_ADAMS_MONIQUE]$ cp 001.mgz > $SUBJECTS_DIR/CON_ADAMS_MONIQUE/mri/orig > > cp: cannot stat `001.mgz': No such file or directory > > > > I don’t know why that happens. > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Pedro Paulo de > Magalhães Oliveira Junior > *Sent:* 17 June 2009 15:14 > *To:* Ahmed, F, Me > *Cc:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] error message > > > > Fatima, > > > > Try this simple procedure to get started. > > > > 1) Convert your dicom files to 001.mgz > > recon-all -i DICOM_FILE_DIR -o 001.mgz > > > > 2) Inside your subjects_dir create a subdirectory like this: > > mkdir -p $SUBJECTS_DIR/test01/mri/orig > > > > 3) copy your 001.mgz into that dir > > cp 001.mgz $SUBJECTS_DIR/test01/mri/orig > > > > 4) run recon-all > > recon-all -s test01 -all > > > > Hope it helps > > > > PPJ > > > > > ----------------------------------------------------------- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > --- Novo Netfilter 3.0 www.Netfilter.com.br > > > 2009/6/17 Ahmed, F, Me <fah...@sun.ac.za> <fah...@sun.ac.za> > > Hello, I am new to using Freesurfer and am trying to run the recon-all > stages in order to get thickness values for brain regions. I have correctly > > converted all my dicom images into the correct mgz format as instructed by > your manual and have carried out motion correction (even though I only have > > one acquisition) to create the orig.mgz file. however, when I try and run > the following command: > > > > "recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 > -s bert" using my subject name, I get the following error message: > > > > [...@localhost DicomImages]$ 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 > > >
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