hmmm, that is puzzling. Can you upload the two subject dirs with the 
rotated direction cosines and I'll take a look?

thanks
Bruce
On Thu, 5 Jun 2014, Alessia 
Giuliano wrote:

> Dear Bruce,
> when I say "the image was rotated" in 2 I mean that I have changed the image header to reflect a new orientation,
> instead in 3 there was an additional image interpolation, therefore a blurring.
> As you said, I can understand that in the latter case things change, but how can be explained so considerable change
> in CC subregions volumes and in CC total volume between case 2 and 1?
> 
> Moreover, we have noticed that the rostrum is sometimes included in the anterior part but othertimes not, is there a
> way to correct this segmentation manually?
> 
> Can you give me any advices to improve the CC segmentation in order to consider the volumes of its subregions to be
> reliable?
> 
> Thank you,
> 
> Alessia Giuliano
> 
> Date: Thu, 5 Jun 2014 08:30:10 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
> 
> Hi  Alessia
> 
> when you say "the image was rotated" do you mean you actually transformed 
> the  image, or you simply changed the image header to reflect a new 
> orientation? I wouldn't think the latter would have a big effect, but the 
> former will involve an additional image interpolation (blurring) and will 
> definitely change things. Same question for 3. Did you include an extra 
> interpolation?
> 
> cheers
> Bruce
>
>
>
>
> 
> On Thu, 5 Jun 2014, Alessia 
> Giuliano wrote:
> 
> > Dear FreeSurefer team,
> > in order to verify the reliability of the volumes of Corpus Callosum (CC) subregions estimated by FreeSurfer
> > I have applied the recon-all on the same subject but in three different situations:
> >  
> > 1. when the image was not preliminarly rotated;
> > 2. when an initial soft rotation was manually performed with SPM;
> > 3. when an initial rigid coregistration in MNI space was performed with SPM.
> > 
> > Although the differences in image orientation between 1, 2 and 3 before the implementation of FreeSurfer
> > were really small, the differences in the volumes of the CC subregions between 1, 2 and 3 are notable.
> > 
> > How can I base on this evident variability my volumetric analysis of CC subregions?
> > 
> > Do you have any suggestions to improve my approach to the CC segmentation?
> > 
> > In order to make my results clear, I attach you a recapitulatory page and I send you a link to the
> > FreeSurfer output in 1, 2 and 3 (https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a).
> > 
> > Thank you,
> > 
> > Alessia Giuliano
> > 
> >
> 
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