Hi Martin,

Unfortunately it is not a single subject, it happens to many.
If I run FS 5.3, I also have to rerun the cross-sectional exploration study, otherwise differences between samples may be explained by different versions of the software.
FYI, no editting was done, except for adjusting watershed parameters for a couple of subjects due to excessive skullstripping. After checking, i reran independent autorecon2+3, base + long for the affected pairs.

I'll get back to you when results of FS 5.3 are available.

Cheers,
Cédric


On 6/28/13 2:43 AM, "Martin Reuter" <mreuter@nmr.mgh.harvard.edu> wrote:

Hi Cedric,

Yes, that is too much difference. Something is going wrong. Is this a single subject or does it happen on many? Can you try FS 5.3 on the subject to see if that fixes it (in a different directory of course)?

It may also be that something goes wrong and needs edits. Or it could be that something got messed up by edits or re-running. So you could also process this subjects from scratch again (all tps cross, then base, then all tps long).

Best, Martin

On 06/25/2013 03:43 PM, Koolschijn, Cédric wrote:
Hi Martin,

Thanks for your fast response.
It makes sense that in the longi-stream results should be more reliable. 

However, it worries me if I see segmentation differences up to 500%, for example amygdala volume going from 1475 to 503 Left and 1595 to 281 for Right, independent vs longitudinal stream respectively.
In the current study we had a cross-sectional exploration study, followed by a longitudinal validation study (so two different samples). The above worries me if we want to compare the cross-sectional results with the longitudinal results, as the differences between independent and longitudinal are in a linear fashion.

Any thoughts on this?

Cheers,
Cédric




From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Date: Tuesday, June 25, 2013 8:00 PM
To: Cédric Koolschijn <P.C.M.P.Koolschijn@uva.nl>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing

Hi Cedric,

this is as expected, the data changes when using the longitudinal stream (it will become more reliable, removing some of the variance you get in the independent processing). Becuase of the different processing approaches, the results from independent processing (cross) and long will not be directly comparable.

Cheers, Martin


On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote:
Hi FreeSurfers,

I ran the longitudinal processing pipeline on my subjects, FS 5.0. 
Following the tutorial, first independently, then base, then long etc. Everything works well,  no problems there.

Out of curiosity I compared the asegstats & aparcstats within subject at baseline (i.e. The same timepoint): so the independent fsid vs the same_fsid.long.same_fsid_template, and there are (large) differences between all volumes/thicknesses. The independent measures are in almost all brain areas larger compared to those derived from the longi-stream. Except for the IC, which is completely the same, but of course, this measure is based on the Buckner method and calculated differently.

Overall this seems a bit strange to me, because I believe there shouldn't be differences within subject on the same time-point. 
Is this the result of the within-subject template use for the longitudinal data or is something else going wrong, or is this normal?

Many thanks!

Cheers,
Cédric

------------------------------------------------------------
P.C.M.P. Koolschijn (Cédric), PhD
Dutch Autism & ADHD Research Center
Brain and Cognition
Amsterdam, The Netherlands W http://www.dutcharc.nl   



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Martin Reuter, Ph.D.
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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: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu