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

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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

--
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