Hi Luigi,

as it affects the surfaces you should rerun the base with

recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ... -white -smooth2 -inflate2 -autorecon3 -curvstats

(replace "..." with additional time points if necessary). That should bring the base up to date.

For the long you should try the same:

recon-all -long <tp?id> <templateID> -white -smooth2 -inflate2 -autorecon3 -curvstats

Disclaimer: this has not been tested in the longitudinal stream. You can test it by running a subject (probably best if it is without edits) through 5.3 and also apply the above fixes to the 5.2 version and compare.

Best, Martin

On 05/08/2013 07:47 AM, Luigi Angelo Maglanoc wrote:

Dear Freesurfer experts,

I have recently read the thread about issues with version 5.2 concerning white surface and pial surface http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28340.html

All of the structural data has been through the longitudinal processing stream using freesurfer version 5.2. I am wondering if it is sufficient to run

recon-all -s <subjid> \ -white \ -autorecon3 \ -nosphere \ -nosurfreg for the base data and the final longitudinal data? Or do I have to rerun the whole longitudinal processing and redo any corrections that have been made?

Thank you in advance!

Sincerely Luigi Maglanoc

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