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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
