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: 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
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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