Re: [Freesurfer] Corpus Callosum segmentation
Dear FreeSurfer team, in order to verify that the segmentation of Corpus Callosum was independent from the initial orientation of the subject MR scan I repeated the recon-all of FreeSurfer in two conditions: 1- when the initial alignement of the scan to the MNI space was gross;2- when the initial alignement of the scan was more precise, but amyway performed manuallly. We found two different results in the CC segmentation and in the resulting volumes of its subregions comparing 1 and 2. How is it possible? I thought that the CC segmentation was performed in the MNI space or with respect to CC eigen axes, but independently from the initial orientation of the scan. Thank you, Alessia Giuliano Date: Mon, 26 May 2014 12:02:26 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Corpus Callosum segmentation Hi Alessia it's tought to tell from a single slice as the subject's head orientation might be a bit slanted. The subregions in the CC are defined purely by the distance along the CC's eigenaxis. cheers Bruce On Mon, 26 May 2014, Alessia Giuliano wrote: > Dear FreeSurfer team, > > I'm intrested in the segmentation of Corpus Callosum and in the volumes of > its subregions. > > Freesurfer divides the Corpus Callosum in 5 subregions but I have noticed an > inconsistency in the boundary that separates the anterior part from the > middle anterior one. > In particular, the Rostrum is sometimes included in the anterior part, but > other times it is included in the middle anterior part, as you can see > comparing the two screenshots that I've attached. > > How much can I consider this parcellation to be reliable? > > 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.
Re: [Freesurfer] Corpus Callosum segmentation reliability
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.
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 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.___ 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.
Re: [Freesurfer] Corpus Callosum segmentation reliability
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 + 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 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
