Dear freesurfer specialists,

I am trying to run the very interesting hippocampus subfield segmentation on 
subjects that have already undergone the standard volumetric pipeline AND the 
longitudinal pipeline. I tried the command "recon-all –subjid <myid> 
-hippo-subfields".
Unfortunately, i'm getting the following output message:

"ERROR: Are you trying to run or re-run a longitudinal time point?
       If so, please specify the following parameters:

       \' -long <tpNid> <templateid> \'

       where <tpNid> is the time point id (SAME as cross sectional
       ID) and <templateid> is the ID created in the -base run.
       The directory <tpNid>.long.<templateid> will be created
       automatically or used for output, if it already exists."

Can I just run the -hippo–subfields command on the already longitudinally 
processed brains, and simply include the flags "-long <tp1id> <templateid>" 
(without "-all") so freesurfer can use the long-directory as output (as it 
states in the error message)? Or do I have to run the -hippo–subfields command 
on the crosssectionally processed brains and include the flags "-long <tp1id> 
<templateid>"? Do I then also need to include the flag –all so that it will do 
the whole longitudinal processing again?

Thank you very very much for your help!

Cheers,
Elisabeth



*******************************

Dipl.-Psych. Elisabeth Wenger

Predoctoral Research Fellow

Center for Lifespan Psychology

MPI for Human Development

Lentzeallee 94, 14195 Berlin, Germany

phone: +49-30-82406-427

web: http://www.mpib-berlin.mpg.de<http://www.mpib-berlin.mpg.de/>
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