External Email - Use Caution Hi Bruce,
You are actually right, wh.mgz has some skull left, this is what is problably causing the inflated surfaces to have so many defects. Thanks for the info. Cheers, Vicente Ferrer Predoctoral Researcher BCBL www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> Sent: Tuesday, November 12, 2019 9:24:59 PM Subject: Re: [Freesurfer] Recon all hard failure, Hi Vicente you can look here for some procedures: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview you should look at the inflated surfaces (including the nofix) as surfaces, not in the slice view. What they look like in the slices is meaningless. The inflated.nofix should show you something large that is wrong like an attachment to the skull. You then need to go into the wm.mgz and see what is causing this and correct it either by manual editing, adding control points, or changing the skull stripping cheers Bruce On Tue, 12 Nov 2019, Vicente Ferrer wrote: > External Email - Use Caution > > Hi Greve, > Yes that is the inflated surface, lets go by parts, so basically the orig > surfaces are actually fine as you can see in the first image here: > > > As for the white surfaces, they haven't been generated because as i explained > freesurfer didn't finished because my job run out of cpu time. I think the > problem starts in the inflated.nofixes surface, I am sending you some > screenshots of them, but my impression is that the image is not properly > aligned to them: > > > I also checked the skull stripping and is fine, I am writing because I > followed the https://fscph.nru.dk/slides/Allison/freesurfer.failure_modes.pdf > slides and this kind of error is definitely not here. As you can see in the > image there is something terribly wrong with inflated.nofix images, basically > right and left side are overlapping. Do you know what could be originating > this? > > Thanks for the help, > Vicente Ferrer > Predoctoral Researcher BCBL > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> > Sent: Tuesday, November 12, 2019 4:46:49 PM > Subject: Re: [Freesurfer] Recon all hard failure, > > And before that you should check the orig and white surfaces > > On 11/12/2019 9:37 AM, Bruce Fischl wrote: > > > Hi Vicente > > I'm not sure what the images are showing - maybe the inflated surface? > That isn't useful to look at in the volume. You should check the > inflated.nofix surface and see if something big is wrong (cerebellum or > skull attached, that kind of thing). There is a tutorial on our wiki for > correcting this kind of defect > > cheers > Bruce > > > > On Tue, 12 Nov 2019, Vicente Ferrer wrote: > > > BQ_BEGIN > External Email - Use Caution > > Hello, > > I was runnning reconall in one of my images and it got stucked fixing surface > defects, since i run it on a cluster it stopped when it runned out from cpu > time. As you will see in the log the command started in SUNday 16 14:59:32 > CEST 2019 and ended in Mon Jun 17 05:10:16 CEST 2019 which is more than usual > for a recon-all duration. I have checked some of the previous images and > there is clearly an alignment problem as you can check in this image: > > > Vicente Ferrer > Predoctoral Researcher BCBL > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > BQ_END > > > _______________________________________________ > 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
