Hi Rashmi

putting them in the orig folder with those numbers will get recon-all to do motion correction and averaging.

cheers Bruce On Thu, 12 Sep 2013, Rashmi Singh wrote:

Hello Freesurfer experts,  I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject.     While running the FreeSurfer, if I want to use the three mprages for that subject as an input file,  may I just keep the three mgz files (001.mgz, 002  .mgz and 003.mgz) in the orig folder and run the simple recon all command :=Recon-all -s (subject file name) -all or do I need to have some additional   l flags so that recon all command will use the three T1 images to get one output file?     Thanks,     Rashmi