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