[Freesurfer] Total cerebral volume.
Hi freesurfer, We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use CortexVol + CorticalWhiteMatterVol + SubCortGrayVol Or CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than "recon-all –long tpN baseID –segstats" and does it affect any other structure or just SupraTentorialVol? Thank you, Zheng Hui ___ 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] Total Cerebral Volume
Hello everyone,Can someone please point out where freesurfer outputs the total cerebral volume (white + gray).Thanks,Anil. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Total cerebral volume.
On 10/24/2012 09:01 AM, Zheng Hui wrote: > > Hi freesurfer, > > We are trying to calculate the total cerebral volume which excludes > cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use > > CortexVol + CorticalWhiteMatterVol + SubCortGrayVol > Or > CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the > list) except ventricle, CSF, cerebellum and brainstem) This should give very close to the same value. I don't think it makes a difference. > > > Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run > the segstats for longitudinal subjects, any extra step other than "recon-all > –long tpN baseID –segstats" and does it affect any other structure or just > SupraTentorialVol? It should not affect other structures. doug > > Thank you, > Zheng Hui > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Total cerebral volume.
Hi Doug,Thanks for replying. But our datasets do showed that Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) is much smaller SubCortGrayVol. The former is only about 30-40% of the later. We are using FS 5.1.0 without the SupraTentorialVol fix.I sent you an aseg file some time ago (the last three columns in the sheet). Can you kindly get back to us so that we can know which volume to use for the total cerebral volume analysis.Thanks,Zheng HuiOn 10/24/2012 09:01 AM, Zheng Hui wrote: > > Hi freesurfer, > > We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use > > CortexVol + CorticalWhiteMatterVol + SubCortGrayVol > Or > CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) This should give very close to the same value. I don't think it makes adifference.> > > Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than "recon-all long tpN baseID segstats" and does it affect any other structure or just SupraTentorialVol? It should not affect other structures. doug ___ 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] Total cerebral volume.
Hi Zheng, there is something wrong with your math. When I sum up all the columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get 215952 for the first row (you get only 67548). Can you double check your calculations? doug On 10/28/2012 11:53 PM, Zheng Hui wrote: > Forgot to attach the excel file. Sorry for that. > > From: zhenghui <mailto:zheng@duke-nus.edu.sg>> > Date: Monday, October 29, 2012 11:52 AM > To: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] Total cerebral volume. > > Hi Doug, > > Thanks for replying. But our datasets do showed that > Sum(all structures (after ICV in the list) except ventricle, CSF, > cerebellum and brainstem) is much smaller SubCortGrayVol. The former > is only about 30-40% of the later. We are using FS 5.1.0 without the > SupraTentorialVol fix.I attached the aseg file for your reference (the > last three columns in the sheet). > > Thanks, > Zheng Hui > > On 10/24/2012 09:01 AM, Zheng Hui wrote: > > > > Hi freesurfer, > > > > We are trying to calculate the total cerebral volume which excludes > cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use > > > > CortexVol + CorticalWhiteMatterVol + SubCortGrayVol > > Or > > CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in > the list) except ventricle, CSF, cerebellum and brainstem) > This should give very close to the same value. I don't think it makes a > difference. > > > > > > Also, I saw Doug's post about the bug fixing for SupraTentorialVol. > To re-run the segstats for longitudinal subjects, any extra step other > than "recon-all –long tpN baseID –segstats" and does it affect any > other structure or just SupraTentorialVol? > It should not affect other structures. > doug -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Total cerebral volume.
Hi Doug, I sum all structures except ventricle, CSF, cerebellum and brainstem in order to compare with SubCortGrayVol. Even the former includes some white matter structures and all subcortical structures, it is smaller compared to SubCortGrayVol. My original question is about calculating the total cerebral volumes, when I found CortexVol + CorticalWhiteMatterVol + SubCortGrayVol is much bigger than CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem). Hope I explained it better this time.Cheers,Zheng HuiOn 11/6/12 2:14 AM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote:Hi Zheng, there is something wrong with your math. When I sum up all the columns in your table from Left-Lateral-Ventricle to CC_Anterior, I get 215952 for the first row (you get only 67548). Can you double check your calculations?dougOn 10/28/2012 11:53 PM, Zheng Hui wrote: Forgot to attach the excel file. Sorry for that. From: zhenghui <zheng@duke-nus.edu.sg <mailto:zheng@duke-nus.edu.sg>> Date: Monday, October 29, 2012 11:52 AM To: Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Total cerebral volume. Hi Doug, Thanks for replying. But our datasets do showed that Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) is much smaller SubCortGrayVol. The former is only about 30-40% of the later. We are using FS 5.1.0 without the SupraTentorialVol fix.I attached the aseg file for your reference (the last three columns in the sheet). Thanks, Zheng Hui On 10/24/2012 09:01 AM, Zheng Hui wrote: > > Hi freesurfer, > > We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use > > CortexVol + CorticalWhiteMatterVol + SubCortGrayVol > Or > CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) This should give very close to the same value. I don't think it makes a difference. > > > Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than "recon-all –long tpN baseID –segstats" and does it affect any other structure or just SupraTentorialVol? It should not affect other structures. doug-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose 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] Total cerebral volume.
Can you send me the aseg.stats file for a single subject where you are seeing this effect? doug On 11/08/2012 03:45 AM, Zheng Hui wrote: > Hi Doug, I sum all structures except ventricle, CSF, cerebellum and > brainstem in order to compare with SubCortGrayVol. Even the former > includes some white matter structures and all subcortical structures, > it is smaller compared to SubCortGrayVol. > > My original question is about calculating the total cerebral volumes, > when I found *CortexVol + CorticalWhiteMatterVol + SubCortGrayVol* is > much bigger than *CortexVol + CorticalWhiteMatterVol + Sum(all > structures (after ICV in the list) except ventricle, CSF, cerebellum > and brainstem)*. > > Hope I explained it better this time. > > Cheers, > Zheng Hui > > On 11/6/12 2:14 AM, "Douglas N Greve" <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Zheng, there is something wrong with your math. When I sum up > all the > columns in your table from Left-Lateral-Ventricle to CC_Anterior, > I get > 215952 for the first row (you get only 67548). Can you double > check your > calculations? > doug > > On 10/28/2012 11:53 PM, Zheng Hui wrote: > > Forgot to attach the excel file. Sorry for that. > > From: zhenghui <mailto:zheng@duke-nus.edu.sg> > <mailto:zheng@duke-nus.edu.sg> > <mailto:zheng@duke-nus.edu.sg%3E>> > Date: Monday, October 29, 2012 11:52 AM > To: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu%3E>> > Subject: [Freesurfer] Total cerebral volume. > > Hi Doug, > > Thanks for replying. But our datasets do showed that > Sum(all structures (after ICV in the list) except ventricle, CSF, > cerebellum and brainstem) is much smaller SubCortGrayVol. The > former > is only about 30-40% of the later. We are using FS 5.1.0 > without the > SupraTentorialVol fix.I attached the aseg file for your > reference (the > last three columns in the sheet). > > Thanks, > Zheng Hui > > On 10/24/2012 09:01 AM, Zheng Hui wrote: > > > > Hi freesurfer, > > > > We are trying to calculate the total cerebral volume which > excludes > cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do > we use > > > > CortexVol + CorticalWhiteMatterVol + SubCortGrayVol > > Or > > CortexVol + CorticalWhiteMatterVol + Sum(all structures > (after ICV in > the list) except ventricle, CSF, cerebellum and brainstem) > This should give very close to the same value. I don't think > it makes a > difference. > > > > > > Also, I saw Doug's post about the bug fixing for > SupraTentorialVol. > To re-run the segstats for longitudinal subjects, any extra > step other > than "recon-all –long tpN baseID –segstats" and does it affect > any > other structure or just SupraTentorialVol? > It should not affect other structures. > doug > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Total Cerebral Volume
Hi Anil, you can just add up the relevant classes in the aseg.stats file Bruce On Thu, 26 Oct 2006, Anil Roy wrote: Hello everyone, Can someone please point out where freesurfer outputs the total cerebral volume (white + gray). Thanks, Anil. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
