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 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 > > > > > > _______________________________________________ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information > in this e-mail is intended only for the > person to whom it is addressed. If you believe this e-mail was sent to you in > error and the e-mail contains patient > information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the > e-mail was sent to you in error but does not contain patient information, > please contact the sender and properly > dispose of the e-mail. > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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