Hi Sue, mri_segstats does not compute the eTIV itself, it just gets it from the transform matrix. doug
On 07/18/2012 09:33 AM, Susan Ruiz wrote: > Hi Bruce, Nick, Muhammad et al., > > I noticed that there is an updated mri_segstats for download in the > release notes on the wiki, but that appears to be for the > SupraTentorial Volume rather than the eTIV. If the patch is available, > that would be greatly appreciated (and preferable to running everyone > through 5.0). Muhammad--thanks for your question about this since we > had not noticed! > > Thanks all, > ~Sue > > * * ** *** ***** ******** ************* > Susan M. M. Ruiz, Ph.D. > Boston University School of Medicine > Laboratory for Neuropsychology > VA Boston Healthcare System > smos...@bu.edu <mailto:smos...@bu.edu> > * * ** *** ***** ******** ************* > > On Jul 17, 2012, at 9:50 AM, Bruce Fischl wrote: > >> Hi Sue >> >> you could take the eTIV from 5.0 and the aparc stats from 5.1.0. I >> believe we already distribute the updated template but it's not used. >> Nick: do you want to send around a patch to recon-all that people can >> use before 5.2 comes out? >> >> thanks >> Bruce >> >> >> On Tue, 17 Jul 2012, Susan Ruiz wrote: >> >>> Hi all, >>> Using previous versions of FreeSurfer, we have used the eTIV as a >>> covariate for our volumetric analyses. We >>> have been using the eTIV numbers from 5.1.0 for new studies. What >>> would you recommend using for subjects who >>> have been run with 5.1.0? Can you make the template available >>> publicly, or would it be legitimate to take the >>> eTIV from 5.0 and the aparc stats from 5.1.0? >>> Thanks, >>> ~Sue >>> * * ** *** ***** ******** ************* >>> Susan M. M. Ruiz, Ph.D. >>> Boston University School of Medicine >>> Laboratory for Neuropsychology >>> VA Boston Healthcare System >>> smos...@bu.edu <mailto:smos...@bu.edu> >>> * * ** *** ***** ******** ************* >>> On Jul 16, 2012, at 4:17 PM, Bruce Fischl wrote: >>> >>> can you send us an example? In the ones we've looked at the >>> older versions were more stable. >>> Alternatively, we can send you a new template that Avi Snyder >>> generated that you could try out >>> >>> cheers >>> Bruce >>> >>> On Mon, 16 Jul 2012, Ayaz, Muhammad wrote: >>> >>> Well, I am using version 5.1.0. I have had same issue in >>> fewer subjects when I used >>> the older version as well. Any comments about that? >>> >>> -----Original Message----- >>> >>> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] >>> >>> Sent: Monday, July 16, 2012 3:04 PM >>> >>> To: Ayaz, Muhammad >>> >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> >>> Subject: Re: [Freesurfer] sum of WM and GM coming out to >>> be bigger than ICV after >>> recon-all >>> >>> Hi Ayaz >>> >>> what version are you running? There appears to be an >>> instability in the >>> >>> eTIV calculation in just version 5.1 (not before or in >>> the upcoming 5.2) >>> >>> cheers >>> >>> Bruce >>> >>> On >>> >>> Mon, 16 Jul 2012, Ayaz, Muhammad wrote: >>> >>> Dear All, >>> >>> >>> >>> After running recon-all, I noticed several subjects >>> that sum of WM and GM >>> is >>> >>> bigger than ICV. I have re-run these subjects and >>> the results is the >>> same >>> >>> sum of GM and WM is coming out to be bigger than ICV. >>> >>> Any suggestions? I need to calculate normalized >>> volumes. >>> >>> >>> >>> Regards >>> >>> Ayaz >>> >>> The information contained in this message and any >>> attachments is intended >>> >>> only for the use of the individual or entity to >>> which it is addressed, >>> and >>> >>> may contain information that is PRIVILEGED, >>> CONFIDENTIAL, and exempt from >>> >>> disclosure under applicable law. If you are not the >>> intended recipient, >>> you >>> >>> are prohibited from copying, distributing, or using >>> the information. >>> Please >>> >>> contact the sender immediately by return e-mail and >>> delete the original >>> >>> message from your system. >>> >>> 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. >>> >>> The information contained in this message and any >>> attachments is intended only for >>> the use of the individual or entity to which it is >>> addressed, and may contain >>> information that is PRIVILEGED, CONFIDENTIAL, and exempt >>> from disclosure under >>> applicable law. If you are not the intended recipient, >>> you are prohibited from >>> copying, distributing, or using the information. Please >>> contact the sender >>> immediately by return e-mail and delete the original >>> message from your system. >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto: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 -- 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
