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.comwrote:
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
- 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
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
- 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?
- 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
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
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?
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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