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 fahmed@sun.ac.za fahmed@sun.ac.za
PPJ,
Thank you for your response, I tried your procedure and got the following message:
[fsl@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-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@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.
- Convert your dicom files to 001.mgz
recon-all -i DICOM_FILE_DIR -o 001.mgz
- Inside your subjects_dir create a subdirectory like this:
mkdir -p $SUBJECTS_DIR/test01/mri/orig
- copy your 001.mgz into that dir
cp 001.mgz $SUBJECTS_DIR/test01/mri/orig
- run recon-all
recon-all -s test01 -all
Hope it helps
PPJ
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br
2009/6/17 Ahmed, F, Me fahmed@sun.ac.za fahmed@sun.ac.za
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly
converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have
one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ 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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