Hi Pietro

what was your recon-all command line? You need to specify different subject identifiers (-s <subject identifier>) for the different datasets

Bruce On Thu, 27 Sep 2012, pietro de rossi wrote:

Hi Freesurfers, I have another quintessentially beginner's problem....

I ran 5 scans through the entire pipeline (-autorecon1 -autorecon2 and -autorecon2 -autorecon-3)

when I check the output going

tksurfer [name_of_folder_with_dcm_files] rh (or lh) inflated

and then

tkmedit [name_of_folder_with_dcm_files] norm.mgz -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

the scans look all the same....it is like the last scan I processed was overwritten on the previous ones....does it make sense?

thank you very much,

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