Hi Michael,

I think you should be fine with option 1. Just make sure that all cross are run with the same version (5.1). It is a little more complicated to keep track of things, but there should be no bias. That way you don't have to worry about edits. 

If you only have very few edits, I would do the clean thing an re-run all data from scratch with 5.3 manually transferring edits only where needed.

Best, Martin

On Jul 9, 2013, at 3:01 PM, "Harms, Michael" <mharms@wustl.edu> wrote:


Hi guys,
We have some longitudinal scans in which the time1 (T1) scans were processed with FS 5.1, and the T2/T3 scans haven't been processed yet.

I'm trying to assess whether the differences between FS 5.1 and 5.3 warrant us re-running the T1 scans under FS 5.3.  
I see two possible options:
1) Process all "cross-sectional" runs under FS 5.1.  i.e., we already have T1 under FS 5.1, so do the cross-runs of T2/T3 under 5.1 as well.  (I'm assuming that it wouldn't be desirable to have a mix of versions at the cross-sectional stage).  Then switch to using FS 5.3 for creating the template (-base) and longitudinal (-long) data.

2) Re-process the cross-sectional scans for T1 using FS 5.3, and do everything with FS 5.3.

Do you have any reason to expect relevant differences in the final -long output between these two approaches?
And, if approach (2) is necessary, do we need to re-run the T1 through FS 5.3 with the "-clean" flag?  i.e,. if we were to re-run the cross-sectional version of the T1 scan using FS 5.3, but keeping previous edits, would that potentially bias the T1 scan in some fashion, since the T2/T3 scans will be run fresh in FS 5.3 without any prior manual edits?

thanks,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mharms@wustl.edu

 

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---------------------------------
Dr. Martin Reuter
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: