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
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/**compliancelinehttp://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.
-- 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
no, it represent the name of the folder that FS will create to put the results of the analysis in. The -i should be the full path to one file in the correct (T1-weighted) dicom series On Thu, 27 Sep 2012, pietro de rossi wrote:
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 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. -- 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-- 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
Thank you very much Bruce! it's working.
2012/9/27 Bruce Fischl fischl@nmr.mgh.harvard.edu
no, it represent the name of the folder that FS will create to put the results of the analysis in. The -i should be the full path to one file in the correct (T1-weighted) dicom series
On Thu, 27 Sep 2012, pietro de rossi wrote:
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 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<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. -- 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-- 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
pietro de rossi