sorry, I didn't realize I hadn't replied to the whole list :-)
so this
recon-all -i <name of one slice in the right dicom series> -s <subject id> -all
is the command for the whole pipeline if I understand correctly.... does <subject id> represents the folder where the dcm files are?
sorry for bothering again..
2012/9/27 Bruce Fischl fischl@nmr.mgh.harvard.edu
can you cc the list on these emails? Your command line should be:
recon-all -i <name of one slice in the right dicom series> -s <subject id> -all
cheers
Bruce
On Thu, 27 Sep 2012, pietro de rossi wrote:
the command line was
recon-all -autorecon1 -autorecon2 -subjid name_of_folder_with_dcm_files
then
recon-all -autorecon2 -autorecon3 -subjid name_of_folder_with_dcm_files
2012/9/27 Bruce Fischl fischl@nmr.mgh.harvard.edu 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 ------------------------------**------- 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
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-- 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