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
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