Hi Elijah,
if you have minimal edits, I'd recommend to reprocess the data from
scratch with 5.3 (that is supposed to be the same as using the -clean
flag when rerunning 5.3 on top of the old 5.0 data). But I'd recommend
to create a new subjectsdir, copy over the subjedid/mri/orig dirs for
each subject and rerun from scratch with 5.3 the independent, base and
long runs.
Best, Martin
On 01/13/2014 06:18 PM, Elijah Mak wrote:
Greetings Freesurfer Community,
I am running a longitudinal study using Freesurfer v.5.3 to compare
rate of cortical thinning between 2 groups of subjects. I hope I can
seek some expert advice on the following situation:
All data (both the baseline and follow-up) has been processed
independently using recon-all. This has been done on Freesurfer 5.0.
Since then, I have upgraded to Freesurfer v5.3 to utilize the linear
mixed effect capability.
For the construction of base and longs, I understand that it is
important to add -clean flag to my recon-all strings to overwrite
brainmask.mgz etc. When must this be done?
I am still new to Freesurer, and I'd greatly appreciate any advice
regarding workflow.
Many Thanks,
Elijah
--
Elijah Mak, B.A.
Doctoral Candidate *|* Psychiatry
University of Cambridge *| *Department of Psychiatry
Trinity College, Cambridge, CB2 1TQ
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--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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