Hi Elisabeth,
the hippo stuff was never tested with the long stream. But I don't see a reason why it should not work. I don't know your command. is subjid the long or the cross subject? Probably you passed the .long. subject and that is why you see that error.
I would recommend to
recon-all -long <tpNid> <templateid> -hippo-subfields
(so run the hippo subfield segementation on the improved longitudinal results instead of the cross sectionals). Let me know how it goes.
Best, Martin
On Tue, 2011-08-30 at 10:44 +0000, Wenger, Elisabeth wrote:
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
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