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 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
Re: [Freesurfer] Corpus Callosum segmentation reliability
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 + 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 ___ Freesurfer mailing list Fr eesur...@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati on 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
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.
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
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.
