Hi Kasper,
It should work (I tried it a while ago with the dev version and it did not crash :-). Could not really tell if it helped much either.
I don't remember if functionality is available in FS5.3 to include that in a long run. In dev, you would include the T2 for both the cross and long run. The long run then takes the T2 from the cross. Not sure if it works passing it directly into a longitudinal run.

Best, Martin

On 05/13/2016 08:43 AM, Bruce Fischl wrote:

Hi Kasper,

I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs.
Bruce
On Fri, 13 May 2016, Kasper Jessen wrote:

Dear FreeSurfer,
Currently, we have only manual edited the BASE (the CROSS was left unedited)
in an longitudinal data. However, some cortical areas (f.eks. such as the
inferior temporal area) are difficult to edit accurately due to image
quality. I then read through the release notes (stable v5.2.0) and found
that a T2/FLAIR can be used to improve the pial surface.

Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial
on the [LONG] runs to get extra improvement of the final pial surfaces?

Best regards,
Kasper Jessen
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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu