Hi Elahe'
I'm surprised it ran that long as it basically failed right away. If you run it as:
recon-all -all -subjid EY
which is what you did, you must put the data in the EY/mri/orig directory. If you want to specify the input volume(s) directly, put -i <input volume> on the command line (more than once if you have more than one volume that you want to motion correct and average).
Not sure why it ran so long with ever step failing, something didn't register the exit codes properly
cheers Bruce
On Fri, 28 Nov 2014, elahe' yargholi wrote:
Dear Freesurfer experts,
I used 'recon-all' command ('recon-all -i path/EYT1.mgz -s EYrecon -all) in freesurfer 4.5 and after 8 hours of process, I received the an error and it stoped.
The error says it can not find files in surf folder... recon-all.log is attached.
I use virtual machine 10- Ubuntu 12.04 - freesurfer 4.5.
I do appreciate your attention.
BR,
Elahe'