Hi Tracy,

if you mean how the method works internally:

the input image is registered to it's left right flipped version and mapped into the midspace. this makes the image upright and straight (see HBM abstract
Robust and Accurate Contralateral Registration for Pose Normalization and Tumor Segmentation. M.Reuter, H.D.Rosas, B.Fischl. Human Brain Mapping 2012, Beijing.
http://reuter.mit.edu/blue/papers/reuter-hbm12-tumor/reuter-hbm12-tumor.pdf

That new image is then taken as the base. The reasoning behind this is:
- the base image gets interpolated similarly to a regular base (with N>1 time points)
- all other steps are identical to the longitudinal workflow (surfaces on the base to initialize the longitudinal time point).

The original publication for the longitudinal pipeline is this
Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis. M.Reuter, N.J.Schmansky, H.D.Rosas, B.Fischl. NeuroImage 61(4):1402-1418, 2012.

but does not describe the single time point situation, which is discussed in:
Statistical Analysis of Longitudinal Neuroimage Data with Linear Mixed Effects Models. J.L.Bernal-Rusiel, D.N.Greve, M.Reuter et al. NeuroImage 66:249-260, 2012.

Best, Martin

On 10/23/2014 12:17 AM, Martin Reuter wrote:
Hi Tracy,
When you call recon-all -base simply pass only the single time point -tp.
Best Martin


Sent via my smartphone, please excuse brevity.

-------- Original message --------
From: Tracy Melzer
Date:10/22/2014 10:59 PM (GMT-05:00)
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal base template creation with one timepoint

Dear FreeSurfer Experts,

I am interested in how the longitudinal stream creates a base template with only a single image. Could someone please explain how or point me to a reference as to how this is accomplished?

Thank you,
Tracy Melzer 



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-- 
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu