Hi Bruce, I re-ran it without running anything else on the machine. Took almost three times as long as my recons usually take but it finished without error. Thank you for your help!
Best, Lily ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Monday, March 30, 2020 5:27 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Recon-all exited with errors Hi Lily that looks ok I think, although it's hard to tell for sure. The cerebellum shouldn't be included in the surface. Are you sure you have enough ram on your machine? It looked like half of it was in use when you ran recon-all. If you want you can tar and gzip the whole subject dir and ftp it to us and we will take a look, but I would try rerunning when nothing else is taking up significant chunks of memory on your machine and see if that fixes it cheers Bruce On Mon, 30 Mar 2020, Wang, Lily wrote: > Hi Dr. Greve, > > I'm not seeing any glaring issues with inclusion of cerebellum or skull in > the surfaces or the mgz. There is a bit of inclusion of the cerebellum in > the wm.mgz. However, two things that do seem strange are 1. a portion of the > subject's cerebellum is black/missing, 2. in the wm.mgz on grayscale, it > looks like the ventricles are supposed to be white, but a big portion of > this subject's ventricles are not included and it seems that it's messing up > the lh.orig.nofix surface as well. Could this possibly be an issue? Please > see attached screenshot. > > Thank you, > Lily > > ____________________________________________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve > <dgr...@mgh.harvard.edu> > Sent: Monday, March 30, 2020 11:55 AM > To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Recon-all exited with errors > It looks like there might be a very large defect. Try looking at the wm.mgz > and brainmask.mgz and the lh.orig.nofix surface to see if there is a large > part of skull or cerebellum that is encompassed in the orig.nofix surface > > On 3/30/2020 11:26 AM, Wang, Lily wrote: > Hi All, > > I have a subject whose T1 quality is quite good but reconstruction > exited with errors so I am not sure what the issue could be. Attached > is the recon-all.log. Could it be that the subject is very old and has > a lot of degeneration? > > Thank you, > Lily > > _______________________________________________ > 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
