Hi Pietro

1. No, you would need 002.mgz etc.. if you had more than 1 scan that you wanted to motion correct and average for that subject/session.

2. The easier way to run recon-all is to use the -i <file> flag, where <file> should be one slice in the proper dicom series (e.g. an mprage). Then you don't need to copy 001.mgz or anything, it will do everything for you.

cheers Bruce

On Wed, 26 Sep 2012, pietro de rossi wrote:

Dear FreeSurfers, I am a beginner, trying to process some 3T MPRAGE scans on my own for a project.

I have a couple of simple questions

1. When I run the recon-all ?autorecon1 ?autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the command works. My question is: do I need to change 001.mgz to 002, 003 an so on for every scan I process?
2. I have to process 3T scans in a .dcm format. Can I just process the scan as it is? Do I have to save the .dcm files as another format, maybe a .mnc file?

thank you very much in advance,

Pietro

-- Pietro De Rossi, MD

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Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma

NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy

Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA