Hi Alessia
I did, and unfortunately I'm not sure there is much I can do. One of the
(long) list of engineering thing we would like to fix is how we deal with
the initial nromalization of subject positioning. At the moment, the scans
you sent me will be resliced differently, and it is that interpolation that
causes the 5% or so differences in CC compartment volumes.
sorry,
Bruce
On Thu, 12 Jun 2014, Alessia Giuliano wrote:
Dear Bruce,
did you see the images that I have sent you?
Thanks,
Alessia Giuliano
____________________________________________________________________________
From: alessia_giuli...@hotmail.it
To: freesurfer@nmr.mgh.harvard.edu
Date: Fri, 6 Jun 2014 06:46:29 +0000
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
Dear Bruce,
the two subject dirs are here
https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a.
The original subject is s50 and the rotated one is rs50.
Thank you very much for your help.
Alessia Giuliano
Date: Thu, 5 Jun 2014 16:27:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability
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 ima
ge header to reflect a new orientation,
> instead in 3 there was an additional image interpolation, therefore a blur
ring.
> As you said, I can understand that in the latter case things change, but h
ow 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 an
terior 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 con
sider the volumes of its subregions to be
> reliable?
>
> Thank you,
>
> Alessia Giuliano
>
> Date: Thu, 5 Jun 2014 08:30:10 -0400
> From: fis...@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 b
etween 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 segmentatio
n?
> >
> > In order to make my results clear, I attach you a recapitulatory page an
d I send you a link to the
> > FreeSurfer output in 1, 2 and 3 (https://www.dropbox.com/sh/k1z5o0e6sq90
qq0/AABx38QxKvxDhUe2lV9imaa9a).
> >
> > Thank you,
> >
> > Alessia Giuliano
> >
> >
>
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