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

---

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.