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

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.