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