Hi Anna, No, you can still use links. When rerunning the base, the cross are not changed. Once the base loiks good, you also have to rerun the longs of course.

Best Martin

Sent via my smartphone, please excuse brevity.

-------- Original message -------- From: Anna Jonsson ajonsson09@gmail.com Date:03/02/2014 5:27 AM (GMT-05:00) To: Martin Reuter mreuter@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal process

Hi thank you for reply. May I ask other question; after editing the base it says to reocnstruct with recon-all -base -tp1 -tp2 etc. Does this require that all scans are located in the same directory? (Before i used symbolic links as scans are in different directories) but i am unsure whether after editing the abse anything further is actually done to the cross runs?

Thank you for your help,

Anna

On Tue, Feb 18, 2014 at 7:58 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Anna,

the linear mixed effects models can include subjects with a single time point and it would be a shame to drop that information. That is why we modified the longitudinal pipeline (use 5.3) to allow processing of subjects with a single time point. However, it is necessary that these images undergo the same processing steps as the rest of the data (to avoid bias). So you run it exactly as other subjects, with a cross sectional, -base and a -long step:

recon-all -all -s <tp1id> -i path_to_tp1_dcm recon-all -base <templateid> -tp <tp1id> -all recon-all -long <tp1id> <templateid> -all

Best, Martin

On 02/18/2014 04:58 AM, Anna Jonsson wrote: Dear Freesurfer experts,

I want to know if possible when doing longitudinal stream to put subjects with only one time-point through the processing (eg base and long runs) in order to subsequently use with the Matlab lme tools? Or better is to leave them out and only do those with 2+ times?

Thank you

Kind Regards,

Anna

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