thank you very much!

2012/9/26 Bruce Fischl fischl@nmr.mgh.harvard.edu

or you could do it all in one command with:

recon-all -i first_dicom_image_name.dcm -s subjID -all

cheers Bruce

On Wed, 26 Sep 2012, Darren Gitelman wrote:

Pietro

...

You should first import your *.dcm files with the command

recon-all -i first_dicom_image_name.dcm -s subjID

Then when you process your data you would type

recon-all -s subjID -autorecon1 -autorecon2

or whatever steps you are using.

Darren

On Wed, Sep 26, 2012 at 9:33 AM, pietro de rossi derossi05@gmail.com 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 ------------------------------**------- 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

-- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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