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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