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.
<div>-------- Original message --------</div><div>From: Tracy Melzer tracy.melzer@otago.ac.nz </div><div>Date:10/22/2014 10:59 PM (GMT-05:00) </div><div>To: freesurfer@nmr.mgh.harvard.edu </div><div>Subject: [Freesurfer] longitudinal base template creation with one timepoint </div><div> </div>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
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://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3458./ 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Martin Reuter