Re: [Freesurfer] eTIV=0.0 on volumes where control points have been added manually
External Email - Use Caution Hi, Thank you for your help. Best regards, Julia Lam 12 jan. 2021 kl. 16:56 skrev Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>: Hi Julia, this is a bug. We've fixed it in our development version, but for you there are a few option. One is that you can just get the value from aseg.stats (asegstats2table). Or you can run recon-all with these flags -talairach -parcstats -parcstats2 -parcstats3 On 12/29/2020 7:34 AM, Julia Lam wrote: External Email - Use Caution Dear all, I received values of 0.0 on variables BrainSegVolNotVent and eTIV when running aparcstats2table on volumes where I've added control points. However, when aseg2stats was used, the variable EstimatedTotalIntraCranialVol was different from 0 on all, including the edited ones. Why is that? I've attached the logfile from one of the subjects where I used control points. I really appreciate any help you can provide. Yours sincerely Julia Lam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1fZEz71vj0N1f00cHXlA7OgPPpOqrL49X2RBla16zYyY_8fCU20J0sTcy1eZBtByA6FA_eLQJVPJuEQNGYxgL2ezk_ZGO2QeRMOUYPFMuxxZxFEnkKFbksjOAaZQ20lOIyRZh0LIash-kODQ8jOxzTJ2eQapn9q_YDxpf5hRXElJ0U7e0ckyMDENvdVgR-ZzTL73T7DHPFIQ5Pz6uC_0MiZJBcWL-S2mNmL4eBb1qPYb27cghQxSjT2m2qqqScqUG/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1fZEz71vj0N1f00cHXlA7OgPPpOqrL49X2RBla16zYyY_8fCU20J0sTcy1eZBtByA6FA_eLQJVPJuEQNGYxgL2ezk_ZGO2QeRMOUYPFMuxxZxFEnkKFbksjOAaZQ20lOIyRZh0LIash-kODQ8jOxzTJ2eQapn9q_YDxpf5hRXElJ0U7e0ckyMDENvdVgR-ZzTL73T7DHPFIQ5Pz6uC_0MiZJBcWL-S2mNmL4eBb1qPYb27cghQxSjT2m2qqqScqUG/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] eTIV=0.0 on volumes where control points have been added manually
External Email - Use Caution Dear all, I received values of 0.0 on variables BrainSegVolNotVent and eTIV when running aparcstats2table on volumes where I've added control points. Why is that? I really appreciate any help you can provide. Yours sincerely Julia Lam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Exited with errors, segmentation fault
External Email - Use Caution Hi, Thank you for your email. Sorry about that. Here they are. Best regards, Julia > 27 okt. 2020 kl. 00:17 skrev Hoopes, Andrew : > > Hi Julia, > I think you might have forgotten to attach the logs :) > Andrew > > On 10/25/20, 11:55 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Julia Lam" julia@mau.se> wrote: > >External Email - Use Caution > >Hi Andrew, >Thank you for your reply. Updating freesurfer solved the problem. However, > when I ran step 2 in the longitudinal processing three subjects exited with > errors. I’ve attached the recon-all.log and recon-all.error. What can I do to > solve this problem? > >Thank you in advance. > >Kind regards, >Julia Lam > >> 20 okt. 2020 kl. 00:17 skrev Hoopes, Andrew : >> >> Hi Julia, >> >> This is a small bug that's been fixed in the 7.1.1 patch release. I would >> recommend updating freesurfer versions (there will be no differences in >> recon-all results). >> >> Best, >> Andrew >> >> On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of >> Julia Lam" > julia@mau.se> wrote: >> >> External Email - Use Caution >> >> Hi, >> In one of 56 volumes, recon-all exited with errors (segmentation fault). I >> tried to rerun but received the same result. How can this be solved? >> >> I’ve attached the recon-all.log and recon-all.error. >> >> I am looking forward to your reply. >> >> Kind regards, >> Julia Lam >> >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >___ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 101_recon-all.error Description: 101_recon-all.error 101_recon-all.log Description: 101_recon-all.log 102_recon-all.error Description: 102_recon-all.error 102_recon-all.log Description: 102_recon-all.log 104_recon-all.error Description: 104_recon-all.error 104_recon-all.log Description: 104_recon-all.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Exited with errors, segmentation fault
External Email - Use Caution Hi Andrew, Thank you for your reply. Updating freesurfer solved the problem. However, when I ran step 2 in the longitudinal processing three subjects exited with errors. I’ve attached the recon-all.log and recon-all.error. What can I do to solve this problem? Thank you in advance. Kind regards, Julia Lam > 20 okt. 2020 kl. 00:17 skrev Hoopes, Andrew : > > Hi Julia, > > This is a small bug that's been fixed in the 7.1.1 patch release. I would > recommend updating freesurfer versions (there will be no differences in > recon-all results). > > Best, > Andrew > > On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Julia Lam" julia@mau.se> wrote: > >External Email - Use Caution > >Hi, >In one of 56 volumes, recon-all exited with errors (segmentation fault). I > tried to rerun but received the same result. How can this be solved? > >I’ve attached the recon-all.log and recon-all.error. > >I am looking forward to your reply. > >Kind regards, >Julia Lam > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
