Hi Fatima,

you can just specify the input dicom(s) with -i to recon-all and it will skip the motion correction if there is only one run.

cheers, Bruce On Wed, 21 Oct 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:

Hello,

I'm currently converting my dicom images into the mgz format and I was wondering, I only have one acquisition per subject, therefore do I have to run the motion correction step before running autorecon1? Or can I just go straight into running autorecon1? From the tutorial, I'd imagine I must run the motion correction step as it says that autorecon1 uses the output from the motion correction step, so I'm just a little confused.

Thank you, Fatima