Dear Martin,
Thank you very much for your reply!
In my initial try i used the .long. subject, exactly.
So, now i will try to use, as you suggested, "recon-all -long <the-crosssectional-subjectid> <the-base-id> -hippo-subfields" and it will then automatically write the hippo-results in the already existing .long. folder, right? I'm really curious to see how this goes.
Thank you so much again, and i'll let you know whether it worked.
Best wishes from Berlin, Elisabeth
Am 01.09.11 18:07 schrieb "Martin Reuter" unter mreuter@nmr.mgh.harvard.edu:
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 -hipposubfields 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 -hipposubfields 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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