Hi Adam,

you shouldn't need to use "-i orig.mgz" when running -autorecon1, this will already use orig.mgz when re-running this step. You should be able to simply use:

recon-all -autorecon1 -s 13667

If you are trying to do something different, and you wish to specify a different input and re-run a subject that is already there you will need to add the flag -force to the command. (and the -i flag requires a full path to the file) So, like this:

recon-all -i /full/path/to/file -autorecon1 -force -s 13667

Jenni

On Tue, 11 Apr 2006, adam walczak wrote:

Hi,

I have been having some basic problems with regard to paths. Freesurfer doesn't seem to want to write to directories that already exist. I was wondering if there is something different I need to do (I am running the reconstruction tutorial) to make this work.

-------- freesurfer-Linux-rh9-stable-pub-v3.0.1 --------

SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects which: recon-all / autorecon1 pwd - /cajal/public/programs/freesurfer/subjects/13667/mri command line - recon-all -i orig.mgz -autorecon1 -s 13667 --------error--------- INFO: SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects ERROR: /cajal/public/programs/freesurfer/subjects/13667 exists

I am at a loss as to why this happens. Any help would be appreciated.

Adam Walczak

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