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